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Gao XJ, Ciura K, Ma Y, Mikolajczyk A, Jagiello K, Wan Y, Gao Y, Zheng J, Zhong S, Puzyn T, Gao X. Toward the Integration of Machine Learning and Molecular Modeling for Designing Drug Delivery Nanocarriers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2407793. [PMID: 39252670 DOI: 10.1002/adma.202407793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/15/2024] [Indexed: 09/11/2024]
Abstract
The pioneering work on liposomes in the 1960s and subsequent research in controlled drug release systems significantly advances the development of nanocarriers (NCs) for drug delivery. This field is evolved to include a diverse array of nanocarriers such as liposomes, polymeric nanoparticles, dendrimers, and more, each tailored to specific therapeutic applications. Despite significant achievements, the clinical translation of nanocarriers is limited, primarily due to the low efficiency of drug delivery and an incomplete understanding of nanocarrier interactions with biological systems. Addressing these challenges requires interdisciplinary collaboration and a deep understanding of the nano-bio interface. To enhance nanocarrier design, scientists employ both physics-based and data-driven models. Physics-based models provide detailed insights into chemical reactions and interactions at atomic and molecular scales, while data-driven models leverage machine learning to analyze large datasets and uncover hidden mechanisms. The integration of these models presents challenges such as harmonizing different modeling approaches and ensuring model validation and generalization across biological systems. However, this integration is crucial for developing effective and targeted nanocarrier systems. By integrating these approaches with enhanced data infrastructure, explainable AI, computational advances, and machine learning potentials, researchers can develop innovative nanomedicine solutions, ultimately improving therapeutic outcomes.
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Affiliation(s)
- Xuejiao J Gao
- Jiangxi Province Key Laboratory of Porous Functional Materials, College of Chemistry and Materials, Jiangxi Normal University, Nanchang, 330022, P. R. China
| | - Krzesimir Ciura
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
- Department of Physical Chemistry, Medical University of Gdansk, Al. Gen. Hallera 107, Gdansk, 80-416, Poland
| | - Yuanjie Ma
- Jiangxi Province Key Laboratory of Porous Functional Materials, College of Chemistry and Materials, Jiangxi Normal University, Nanchang, 330022, P. R. China
| | - Alicja Mikolajczyk
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Karolina Jagiello
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Yuxin Wan
- Jiangxi Province Key Laboratory of Porous Functional Materials, College of Chemistry and Materials, Jiangxi Normal University, Nanchang, 330022, P. R. China
| | - Yurou Gao
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiajia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China
| | - Shengliang Zhong
- Jiangxi Province Key Laboratory of Porous Functional Materials, College of Chemistry and Materials, Jiangxi Normal University, Nanchang, 330022, P. R. China
| | - Tomasz Puzyn
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China
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2
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Tavakoli A, Hu S, Ebrahim S, Kachar B. Hemifusomes and Interacting Proteolipid Nanodroplets: Formation of a Novel Cellular Organelle Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610112. [PMID: 39253452 PMCID: PMC11383319 DOI: 10.1101/2024.08.28.610112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Within cells, vesicle fusion, scission, and the formation of intraluminal vesicles are critical processes that facilitate traffic, degradation, and recycling of cellular components, and maintenance of cellular homeostasis. Despite significant advancements in elucidating the molecular mechanisms that drive these dynamic processes, the direct in situ visualization of membrane remodeling intermediates remains challenging. Here, through the application of cryo-electron tomography in mammalian cells, we have identified a previously undescribed vesicular organelle complex with unique membrane topology: heterotypic hemifused vesicles that share extended hemifusion diaphragms (HDs) with a 42 nm proteolipid nanodroplet (PND) at their rim. We have termed these organelle complexes "hemifusomes". The HDs of hemifusomes exhibit a range of sizes and curvatures, including the formation of lens-shaped compartments encapsulated within the membrane bilayer. The morphological diversity of the lens-shaped vesicle aligns with a step-wise process of their intraluminal budding, ultimately leading to their scission and the generation of intraluminal vesicles. We propose that hemifusomes function as versatile platforms for protein and lipid sorting and as central hubs for the biogenesis of intraluminal vesicles and the formation of multivesicular bodies.
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3
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Alimohamadi H, Luo EWC, Yang R, Gupta S, Nolden KA, Mandal T, Blake Hill R, Wong GCL. Dynamins combine mechano-constriction and membrane remodeling to enable two-step mitochondrial fission via a 'snap-through' instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608723. [PMID: 39229060 PMCID: PMC11370335 DOI: 10.1101/2024.08.19.608723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Mitochondrial fission is controlled by dynamin proteins, the dysregulation of which is correlated with diverse diseases. Fission dynamins are GTP hydrolysis-driven mechanoenzymes that self-oligomerize into helical structures that constrict membrane to achieve fission, but details are not well understood. However, dynamins can also remodel membranes by inducing negative Gaussian curvature, the type of curvature required for completion of fission. Here, we examine how these drastically different mechanisms synergistically exert their influences on a membrane, via a mechanical model calibrated with small-angle X-ray scattering structural data. We find that free dynamin can trigger a "snap-through instability" that enforces a shape transition from an oligomer-confined cylindrical membrane to a drastically narrower catenoid-shaped neck within the spontaneous hemi-fission regime, in a manner that depends critically on the length of the confined tube. These results indicate how the combination of dynamin assembly, and paradoxically disassembly, can lead to diverse pathways to scission.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90025, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Elizabeth Wei-Chia Luo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90025, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Rena Yang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90025, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Kelsey A Nolden
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, CO, 80045, USA
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90025, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
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4
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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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5
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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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6
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing Multifunctional Viral and Eukaryotic Proteins for Generating Scission Necks in Membranes. ACS NANO 2024; 18:15545-15556. [PMID: 38838261 DOI: 10.1021/acsnano.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is M2 viroporin, a proton pump from the influenza A virus that is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging small-angle X-ray scattering structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemifission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Wei-Chia Luo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Rena Yang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90025, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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7
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Liu Y, Xiao W, Xiao X, Wang H, Peng R, Feng Y, Zhao Q, Pan F. Dynamic tracking of onion-like carbon nanoparticles in cancer cells using limited-angle holographic tomography with self-supervised learning. BIOMEDICAL OPTICS EXPRESS 2024; 15:3076-3091. [PMID: 38855692 PMCID: PMC11161346 DOI: 10.1364/boe.522563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 06/11/2024]
Abstract
This research presents a novel approach for the dynamic monitoring of onion-like carbon nanoparticles inside colorectal cancer cells. Onion-like carbon nanoparticles are widely used in photothermal cancer therapy, and precise 3D tracking of their distribution is crucial. We proposed a limited-angle digital holographic tomography technique with unsupervised learning to achieve rapid and accurate monitoring. A key innovation is our internal learning neural network. This network addresses the information limitations of limited-angle measurements by directly mapping coordinates to measured data and reconstructing phase information at unmeasured angles without external training data. We validated the network using standard SiO2 microspheres. Subsequently, we reconstructed the 3D refractive index of onion-like carbon nanoparticles within cancer cells at various time points. Morphological parameters of the nanoparticles were quantitatively analyzed to understand their temporal evolution, offering initial insights into the underlying mechanisms. This methodology provides a new perspective for efficiently tracking nanoparticles within cancer cells.
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Affiliation(s)
- Yakun Liu
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
| | - Wen Xiao
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
| | - Xi Xiao
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Hao Wang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Ran Peng
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Yuchen Feng
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Zhao
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Feng Pan
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
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8
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Spencer RKW, Santos-Pérez I, Rodríguez-Renovales I, Martinez Galvez JM, Shnyrova AV, Müller M. Membrane fission via transmembrane contact. Nat Commun 2024; 15:2793. [PMID: 38555357 PMCID: PMC10981662 DOI: 10.1038/s41467-024-47122-w] [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: 05/10/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Division of intracellular organelles often correlates with additional membrane wrapping, e.g., by the endoplasmic reticulum or the outer mitochondrial membrane. Such wrapping plays a vital role in proteome and lipidome organization. However, how an extra membrane impacts the mechanics of the division has not been investigated. Here we combine fluorescence and cryo-electron microscopy experiments with self-consistent field theory to explore the stress-induced instabilities imposed by membrane wrapping in a simple double-membrane tubular system. We find that, at physiologically relevant conditions, the outer membrane facilitates an alternative pathway for the inner-tube fission through the formation of a transient contact (hemi-fusion) between both membranes. A detailed molecular theory of the fission pathways in the double membrane system reveals the topological complexity of the process, resulting both in leaky and leakless intermediates, with energies and topologies predicting physiological events.
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Affiliation(s)
- Russell K W Spencer
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany.
| | - Isaac Santos-Pérez
- Electron Microscopy and Crystallography Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Izaro Rodríguez-Renovales
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena, Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Anna V Shnyrova
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany.
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9
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Alimohamadi H, Luo EWC, Gupta S, de Anda J, Yang R, Mandal T, Wong GCL. Comparing multifunctional viral and eukaryotic proteins for generating scission necks in membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574447. [PMID: 38260291 PMCID: PMC10802413 DOI: 10.1101/2024.01.05.574447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example is the M2 viroporin, a proton pump from the influenza A virus which is multiplexed with membrane remodeling activity to induce budding and scission in the host membrane during viral maturation. In comparison, the dynamin family constitutes a class of eukaryotic proteins implicated in mitochondrial fission, as well as various budding and endocytosis pathways. In the case of Dnm1, the mitochondrial fission protein in yeast, the membrane remodeling activity is multiplexed with mechanoenzyme activity to create fission necks. It is not clear why these functions are combined in these scission processes, which occur in drastically different compositions and solution conditions. In general, direct experimental access to changing neck sizes induced by individual proteins or peptide fragments is challenging due to the nanoscale dimensions and influence of thermal fluctuations. Here, we use a mechanical model to estimate the size of scission necks by leveraging Small-Angle X-ray Scattering (SAXS) structural data of protein-lipid systems under different conditions. The influence of interfacial tension, lipid composition, and membrane budding morphology on the size of the induced scission necks is systematically investigated using our data and molecular dynamic simulations. We find that the M2 budding protein from the influenza A virus has robust pH-dependent membrane activity that induces nanoscopic necks within the range of spontaneous hemi-fission for a broad range of lipid compositions. In contrast, the sizes of scission necks generated by mitochondrial fission proteins strongly depend on lipid composition, which suggests a role for mechanical constriction.
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10
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Pérez-Jover I, Rochon K, Hu D, Mahajan M, Madan Mohan P, Santos-Pérez I, Ormaetxea Gisasola J, Martinez Galvez JM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nat Commun 2024; 15:52. [PMID: 38168038 PMCID: PMC10761769 DOI: 10.1038/s41467-023-44413-6] [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: 07/02/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mukesh Mahajan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Isaac Santos-Pérez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology, Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, 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
| | - Jason A Mears
- Department of Pharmacology, 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
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anna V Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain.
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain.
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, 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.
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11
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De Franceschi N, Barth R, Meindlhumer S, Fragasso A, Dekker C. Dynamin A as a one-component division machinery for synthetic cells. NATURE NANOTECHNOLOGY 2024; 19:70-76. [PMID: 37798563 DOI: 10.1038/s41565-023-01510-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/08/2023] [Indexed: 10/07/2023]
Abstract
Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division machinery for synthetic cells. Here we use fluorescence microscopy and fluorescence recovery after photobleaching measurements to study the in vitro reconstitution of the bacterial protein dynamin A inside liposomes. Upon external reshaping of the liposomes into dumbbells, dynamin A self-assembles at the membrane neck, resulting in membrane hemi-scission and even full scission. Dynamin A proteins constitute a simple one-component division machinery capable of splitting dumbbell-shaped liposomes, marking an important step towards building a synthetic cell.
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Affiliation(s)
- Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- IMol Polish Academy of Sciences, Warsaw, Poland
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Sabrina Meindlhumer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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12
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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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13
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Khurana H, Pucadyil TJ. "Gearing" up for dynamin-catalyzed membrane fission. Curr Opin Cell Biol 2023; 83:102204. [PMID: 37451176 DOI: 10.1016/j.ceb.2023.102204] [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: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Endocytic dynamins self-assemble into helical scaffolds and utilize energy from GTP hydrolysis to constrict and sever tubular membranous necks of budded endocytic intermediates. They bind the membrane using a pleckstrin-homology domain (PHD). The PHD is characterized by four unstructured loops, two of which partially insert into the membrane. Recent studies reveal that loop insertion lowers the bending rigidity of the membrane and that mutations in these two loops produce separable and opposite effects on the efficiency of dynamin-catalyzed membrane fission. Here, we review the current understanding of dynamin-catalyzed membrane fission and attempt to reconcile contrasting notions that have emerged from biochemical and cellular studies evaluating the role of the PHD in this process. We propose that two membrane-inserting loops act as "gears" that define the catalytic efficiency of the dynamin helical scaffold in membrane fission.
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Affiliation(s)
- Himani Khurana
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Thomas J Pucadyil
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India.
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14
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Pérez-Jover I, Rochon K, Hu D, Mohan PM, Santos-Perez I, Gisasola JO, Galvez JMM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1-catalyzed mitochondrial fission through a conserved disordered C-terminal Short Linear Motif. RESEARCH SQUARE 2023:rs.3.rs-3161608. [PMID: 37503116 PMCID: PMC10371074 DOI: 10.21203/rs.3.rs-3161608/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial fission, but the regulatory mechanisms remain ambiguous. Here we found that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, leading to the fission of model membranes in vitro. In vivo, the availability of the native CT-SLiM is a requirement for productive mitochondrial fission, as both non-native extension and deletion of the CT-SLiM severely impair its progression. Thus, contrary to prevailing models, Drp1-catalyzed mitochondrial fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Isaac Santos-Perez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, 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
| | - Jason A Mears
- Department of Pharmacology, 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
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anna V Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, 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
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15
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Lau YMA, Pang J, Tilstra G, Couture-Senécal J, Khan OF. The engineering challenges and opportunities when designing potent ionizable materials for the delivery of ribonucleic acids. Expert Opin Drug Deliv 2022; 19:1650-1663. [PMID: 36377494 DOI: 10.1080/17425247.2022.2144827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Ionizable lipids are critical components in lipid nanoparticles. These molecules sequester nucleic acids for delivery to cells. However, to build more efficacious delivery molecules, the field must continue to broaden structure-function studies for greater insight. While nucleic acid-binding efficiency, degradability and nanoparticle stability are vitally important, this review offers perspective on additional factors that must be addressed to improve delivery efficiency. AREAS COVERED We discuss how administration route, cellular heterogeneity, uptake pathway, endosomal escape timing, age, sex, and threshold effects can change depending on the type of LNP ionizable lipid. EXPERT OPINION Ionizable lipid structure-function studies often focus on the efficiency of RNA utilization and biodistribution. While these focus areas are critical, they remain high-level observations. As our tools for observation and system interrogation improve, we believe that the field should begin collecting additional data. At the cellular level, this data should include age (dividing or senescent cells), sex and phenotype, cell entry pathway, and endosome type. Additionally, administration route and dose are essential to track. This additional data will allow us to identify and understand heterogeneity in LNP efficacy across patient populations, which will help us provide better ionizable lipid options for different groups.
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Affiliation(s)
- Yan Ming Anson Lau
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Janice Pang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Grayson Tilstra
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | | | - Omar F Khan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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16
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Abstract
Atlastin (ATL) GTPases undergo trans dimerization and a power strokelike crossover conformational rearrangement to drive endoplasmic reticulum membrane fusion. Fusion depends on GTP, but the role of nucleotide hydrolysis has remained controversial. For instance, nonhydrolyzable GTP analogs block fusion altogether, suggesting a requirement for GTP hydrolysis in ATL dimerization and crossover, but this leaves unanswered the question of how the ATL dimer is disassembled after fusion. We recently used the truncated cytoplasmic domain of wild-type Drosophila ATL (DATL) and a novel hydrolysis-deficient D127N variant in single turnover assays to reveal that dimerization and crossover consistently precede GTP hydrolysis, with hydrolysis coinciding more closely with dimer disassembly. Moreover, while nonhydrolyzable analogs can bind the DATL G domain, they fail to fully recapitulate the GTP-bound state. This predicted that nucleotide hydrolysis would be dispensable for fusion. Here we report that the D127N variant of full-length DATL drives both outer and inner leaflet membrane fusion with little to no detectable hydrolysis of GTP. However, the trans dimer fails to disassemble and subsequent rounds of fusion fail to occur. Our findings confirm that ATL mediated fusion is driven in the GTP-bound state, with nucleotide hydrolysis serving to reset the fusion machinery for recycling.
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Affiliation(s)
- Daniel Crosby
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tina H. Lee
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213,*Address correspondence to: Tina H. Lee ()
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17
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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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18
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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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19
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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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20
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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: 30] [Impact Index Per Article: 10.0] [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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21
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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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22
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Xu YF, Chen X, Yang Z, Xiao P, Liu CH, Li KS, Yang XZ, Wang YJ, Zhu ZL, Xu ZG, Zhang S, Wang C, Song YC, Zhao WD, Wang CH, Ji ZL, Zhang ZY, Cui M, Sun JP, Yu X. PTP-MEG2 regulates quantal size and fusion pore opening through two distinct structural bases and substrates. EMBO Rep 2021; 22:e52141. [PMID: 33764618 DOI: 10.15252/embr.202052141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/26/2021] [Accepted: 02/18/2021] [Indexed: 02/02/2023] Open
Abstract
Tyrosine phosphorylation of secretion machinery proteins is a crucial regulatory mechanism for exocytosis. However, the participation of protein tyrosine phosphatases (PTPs) in different exocytosis stages has not been defined. Here we demonstrate that PTP-MEG2 controls multiple steps of catecholamine secretion. Biochemical and crystallographic analyses reveal key residues that govern the interaction between PTP-MEG2 and its substrate, a peptide containing the phosphorylated NSF-pY83 site, specify PTP-MEG2 substrate selectivity, and modulate the fusion of catecholamine-containing vesicles. Unexpectedly, delineation of PTP-MEG2 mutants along with the NSF binding interface reveals that PTP-MEG2 controls the fusion pore opening through NSF independent mechanisms. Utilizing bioinformatics search and biochemical and electrochemical screening approaches, we uncover that PTP-MEG2 regulates the opening and extension of the fusion pore by dephosphorylating the DYNAMIN2-pY125 and MUNC18-1-pY145 sites. Further structural and biochemical analyses confirmed the interaction of PTP-MEG2 with MUNC18-1-pY145 or DYNAMIN2-pY125 through a distinct structural basis compared with that of the NSF-pY83 site. Our studies thus provide mechanistic insights in complex exocytosis processes.
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Affiliation(s)
- Yun-Fei Xu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.,Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xu Chen
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, Shandong University School of Medicine, Jinan, China
| | - Zhao Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Chun-Hua Liu
- Department of Physiology, Shandong First Medical University, Taian, China
| | - Kang-Shuai Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.,Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao-Zhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yi-Jing Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Zhong-Liang Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhi-Gang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, China
| | - Sheng Zhang
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
| | - Chuan Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - You-Chen Song
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Wei-Dong Zhao
- Department of Developmental Cell Biology, China Medical University, Shenyang, China
| | - Chang-He Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhong-Yin Zhang
- Departments of Medicinal Chemistry and Molecular Pharmacology and of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA
| | - Min Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, Shandong University School of Medicine, Jinan, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, Shandong University School of Medicine, Jinan, China
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23
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Torres-Vanegas JD, Cruz JC, Reyes LH. Delivery Systems for Nucleic Acids and Proteins: Barriers, Cell Capture Pathways and Nanocarriers. Pharmaceutics 2021; 13:428. [PMID: 33809969 PMCID: PMC8004853 DOI: 10.3390/pharmaceutics13030428] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022] Open
Abstract
Gene therapy has been used as a potential approach to address the diagnosis and treatment of genetic diseases and inherited disorders. In this line, non-viral systems have been exploited as promising alternatives for delivering therapeutic transgenes and proteins. In this review, we explored how biological barriers are effectively overcome by non-viral systems, usually nanoparticles, to reach an efficient delivery of cargoes. Furthermore, this review contributes to the understanding of several mechanisms of cellular internalization taken by nanoparticles. Because a critical factor for nanoparticles to do this relies on the ability to escape endosomes, researchers have dedicated much effort to address this issue using different nanocarriers. Here, we present an overview of the diversity of nanovehicles explored to reach an efficient and effective delivery of both nucleic acids and proteins. Finally, we introduced recent advances in the development of successful strategies to deliver cargoes.
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Affiliation(s)
- Julian D. Torres-Vanegas
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
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24
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Smirnova YG, Müller M. How does curvature affect the free-energy barrier of stalk formation? Small vesicles vs apposing, planar membranes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:253-264. [PMID: 33547940 PMCID: PMC8071802 DOI: 10.1007/s00249-020-01494-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/08/2020] [Accepted: 12/31/2020] [Indexed: 11/26/2022]
Abstract
Using molecular simulations of POPC lipids in conjunction with the calculation of the Minimum Free-Energy Path (MFEP), we study the effect of strong membrane curvature on the formation of the first fusion intermediate-the stalk between a vesicle and its periodic image. We find that the thermodynamic stability of this hourglass-shaped, hydrophobic connection between two vesicles is largely increased by the strong curvature of small vesicles, whereas the intrinsic barrier to form a stalk, i.e., associated with dimple formation and lipid tails protrusions, is similar to the case of two, apposing, planar membranes. A significant reduction of the barrier of stalk formation, however, stems from the lower dehydration free energy that is required to bring highly curved vesicle into a distance, at which stalk formation may occur, compared to the case of apposing, planar membranes.
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Affiliation(s)
- Y G Smirnova
- Institute for Theoretical Physics, Georg-August University, 37077, Göttingen, Germany.
| | - M Müller
- Institute for Theoretical Physics, Georg-August University, 37077, Göttingen, Germany
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25
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Arai N, Koishi T, Ebisuzaki T. Nanotube Active Water Pump Driven by Alternating Hydrophobicity. ACS NANO 2021; 15:2481-2489. [PMID: 33534546 DOI: 10.1021/acsnano.0c06493] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Water transport must be efficiency controlled for the future sustainability of life. Various water transport systems using carbon nanotubes have been proposed in recent years. Although these systems are more permeable than aquaporins, their water transport is passive. In this study, we successfully demonstrate an active water pump driven by simple hydrophobic interaction through computer simulation. Even in the absence of a pressure- or density-gradient, the proposed pump can actively transport water molecules by alternately switching the hydrophobicity of the pump surface. The water transport rate can be easily controlled by varying the time interval of switching. The pump with optimized switching time exhibits prominent water permeance. The results obtained herein can be applied in various water transport technologies because of the simple mechanics. The proposed water pump has the potential to realize an effective device such as a low-energy artificial purification system.
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Affiliation(s)
- Noriyoshi Arai
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
- Computational Astrophysics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Takahiro Koishi
- Department of Applied Physics, University of Fukui, Bunkyo, Fukui 910-8507, Japan
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26
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Golani G, Leikina E, Melikov K, Whitlock JM, Gamage DG, Luoma-Overstreet G, Millay DP, Kozlov MM, Chernomordik LV. Myomerger promotes fusion pore by elastic coupling between proximal membrane leaflets and hemifusion diaphragm. Nat Commun 2021; 12:495. [PMID: 33479215 PMCID: PMC7820291 DOI: 10.1038/s41467-020-20804-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Myomerger is a muscle-specific membrane protein involved in formation of multinucleated muscle cells by mediating the transition from the early hemifusion stage to complete fusion. Here, we considered the physical mechanism of the Myomerger action based on the hypothesis that Myomerger shifts the spontaneous curvature of the outer membrane leaflets to more positive values. We predicted, theoretically, that Myomerger generates the outer leaflet elastic stresses, which propagate into the hemifusion diaphragm and accelerate the fusion pore formation. We showed that Myomerger ectodomain indeed generates positive spontaneous curvature of lipid monolayers. We substantiated the mechanism by experiments on myoblast fusion and influenza hemagglutinin-mediated cell fusion. In both processes, the effects of Myomerger ectodomain were strikingly similar to those of lysophosphatidylcholine known to generate a positive spontaneous curvature of lipid monolayers. The control of post-hemifusion stages by shifting the spontaneous curvature of proximal membrane monolayers may be utilized in diverse fusion processes.
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Affiliation(s)
- Gonen Golani
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Evgenia Leikina
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kamran Melikov
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jarred M Whitlock
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dilani G Gamage
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Gracia Luoma-Overstreet
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Leonid V Chernomordik
- Section on Membrane Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Profile of Sandra L. Schmid. Proc Natl Acad Sci U S A 2020; 117:31563-31566. [PMID: 33257559 DOI: 10.1073/pnas.2022997117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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28
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Gao S, Hu J. Mitochondrial Fusion: The Machineries In and Out. Trends Cell Biol 2020; 31:62-74. [PMID: 33092941 DOI: 10.1016/j.tcb.2020.09.008] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 11/15/2022]
Abstract
Mitochondria are highly dynamic organelles that constantly undergo fission and fusion. Disruption of mitochondrial dynamics undermines their function and causes several human diseases. The fusion of the outer (OMM) and inner mitochondrial membranes (IMM) is mediated by two classes of dynamin-like protein (DLP): mitofusin (MFN)/fuzzy onions 1 (Fzo1) and optic atrophy 1/mitochondria genome maintenance 1 (OPA1/Mgm1). Given the lack of structural information on these fusogens, the molecular mechanisms underlying mitochondrial fusion remain unclear, even after 20 years. Here, we review recent advances in structural studies of the mitochondrial fusion machinery, discuss their implication for DLPs, and summarize the pathogenic mechanisms of disease-causing mutations in mitochondrial fusion DLPs.
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Affiliation(s)
- Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, 510530 Guangzhou, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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29
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Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. Int J Mol Sci 2020; 21:ijms21197298. [PMID: 33023247 PMCID: PMC7582872 DOI: 10.3390/ijms21197298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Synapses play a central role for the processing of information in the brain and have been analyzed in countless biochemical, electrophysiological, imaging, and computational studies. The functionality and plasticity of synapses are nevertheless still difficult to predict, and conflicting hypotheses have been proposed for many synaptic processes. In this review, we argue that the cause of these problems is a lack of understanding of the spatiotemporal dynamics of key synaptic components. Fortunately, a number of emerging imaging approaches, going beyond super-resolution, should be able to provide required protein positions in space at different points in time. Mathematical models can then integrate the resulting information to allow the prediction of the spatiotemporal dynamics. We argue that these models, to deal with the complexity of synaptic processes, need to be designed in a sufficiently abstract way. Taken together, we suggest that a well-designed combination of imaging and modelling approaches will result in a far more complete understanding of synaptic function than currently possible.
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30
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Massana Muñoz X, Kretz C, Silva-Rojas R, Ochala J, Menuet A, Romero NB, Cowling BS, Laporte J. Physiological impact and disease reversion for the severe form of centronuclear myopathy linked to dynamin. JCI Insight 2020; 5:137899. [PMID: 32809972 PMCID: PMC7526554 DOI: 10.1172/jci.insight.137899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/12/2020] [Indexed: 11/17/2022] Open
Abstract
Classical dynamins are large GTPases regulating membrane and cytoskeleton dynamics, and they are linked to different pathological conditions ranging from neuromuscular diseases to encephalopathy and cancer. Dominant dynamin 2 (DNM2) mutations lead to either mild adult onset or severe autosomal dominant centronuclear myopathy (ADCNM). Our objectives were to better understand the pathomechanism of severe ADCNM and test a potential therapy. Here, we created the Dnm2SL/+ mouse line harboring the common S619L mutation found in patients with severe ADCNM and impairing the conformational switch regulating dynamin self-assembly and membrane remodeling. The Dnm2SL/+ mouse faithfully reproduces severe ADCNM hallmarks with early impaired muscle function and force, together with myofiber hypotrophy. It revealed swollen mitochondria lacking cristae as the main ultrastructural defect and potential cause of the disease. Patient analysis confirmed this structural hallmark. In addition, DNM2 reduction with antisense oligonucleotides after disease onset efficiently reverted locomotor and force defects after only 3 weeks of treatment. Most histological defects including mitochondria alteration were partially or fully rescued. Overall, this study highlights an efficient approach to revert the severe form of dynamin-related centronuclear myopathy. These data also reveal that the dynamin conformational switch is key for muscle function and should be targeted for future therapeutic developments. The dynamin 2 S619L mouse model displays defects in skeletal muscle that are rescued by reducing dynamin 2 protein levels with antisense oligonucleotide treatment.
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Affiliation(s)
- Xènia Massana Muñoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Christine Kretz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Roberto Silva-Rojas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Ochala
- Centre of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Alexia Menuet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Norma B Romero
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, Paris, France.,Sorbonne Université, AP-HP, INSERM, Centre de référence des maladies neuromusculaires Nord/Est/Ile de France, Paris, France
| | - Belinda S Cowling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Dynacure, Illkirch, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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31
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Ranjbari E, Taleat Z, Mapar M, Aref M, Dunevall J, Ewing A. Direct Measurement of Total Vesicular Catecholamine Content with Electrochemical Microwell Arrays. Anal Chem 2020; 92:11325-11331. [PMID: 32692153 DOI: 10.1021/acs.analchem.0c02010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have designed and fabricated a microwell array chip (MWAC) to trap and detect the entire content of individual vesicles after disruption of the vesicular membrane by an applied electrical potential. To understand the mechanism of vesicle impact electrochemical cytometry (VIEC) in microwells, we simulated the rupture of the vesicles and subsequent diffusion of entrapped analytes. Two possibilities were tested: (i) the vesicle opens toward the electrode, and (ii) the vesicle opens away from the electrode. These two possibilities were simulated in the different microwells with varied depth and width. Experimental VIEC measurements of the number of molecules for each vesicle in the MWAC were compared to VIEC on a gold microdisk electrode as a control, and the quantified catecholamines between these two techniques was the same. We observed a prespike foot in a significant number of events (∼20%) and argue this supports the hypothesis that the vesicles rupture toward the electrode surface with a more complex mechanism including the formation of a stable pore intermediate. This study not only confirms that in standard VIEC experiments the whole content of the vesicle is oxidized and quantified at the surface of the microdisk electrode but actively verifies that the adsorbed vesicle on the surface of the electrode forms a pore in the vicinity of the electrode rather than away from it. The fabricated MWAC promotes our ability to quantify the content of vesicles accurately, which is fundamentally important in bioanalysis of the vesicles.
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Affiliation(s)
- Elias Ranjbari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Zahra Taleat
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mokhtar Mapar
- Division of Biological Physics, Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Mohaddeseh Aref
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Andrew Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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32
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Bashkirov PV, Kuzmin PI, Chekashkina K, Arrasate P, Vera Lillo J, Shnyrova AV, Frolov VA. Reconstitution and real-time quantification of membrane remodeling by single proteins and protein complexes. Nat Protoc 2020; 15:2443-2469. [PMID: 32591769 PMCID: PMC10839814 DOI: 10.1038/s41596-020-0337-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/14/2020] [Indexed: 02/08/2023]
Abstract
Cellular membrane processes, from signal transduction to membrane fusion and fission, depend on acute membrane deformations produced by small and short-lived protein complexes working in conditions far from equilibrium. Real-time monitoring and quantitative assessment of such deformations are challenging; hence, mechanistic analyses of the protein action are commonly based on ensemble averaging, which masks important mechanistic details of the action. In this protocol, we describe how to reconstruct and quantify membrane remodeling by individual proteins and small protein complexes in vitro, using an ultra-short (80- to 400-nm) lipid nanotube (usNT) template. We use the luminal conductance of the usNT as the real-time reporter of the protein interaction(s) with the usNT. We explain how to make and calibrate the usNT template to achieve subnanometer precision in the geometrical assessment of the molecular footprints on the nanotube membrane. We next demonstrate how membrane deformations driven by purified proteins implicated in cellular membrane remodeling can be analyzed at a single-molecule level. The preparation of one usNT takes ~1 h, and the shortest procedure yielding the basic geometrical parameters of a small protein complex takes 10 h.
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Affiliation(s)
- Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudnyy, Russia.
| | - Peter I Kuzmin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia Chekashkina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Pedro Arrasate
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Javier Vera Lillo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Anna V Shnyrova
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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33
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Endter LJ, Smirnova Y, Risselada HJ. Density Field Thermodynamic Integration (DFTI): A "Soft" Approach to Calculate the Free Energy of Surfactant Self-Assemblies. J Phys Chem B 2020; 124:6775-6785. [PMID: 32631061 DOI: 10.1021/acs.jpcb.0c03982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermodynamic integration is one of the most established methods to quantify excess free energies between different metastable states. Excess intermolecular interactions in surfactant assemblies are on the scale of the energy of thermal fluctuations. Therefore, these materials can be deformed and topologically altered via relatively small mechanical stresses. It is thus intuitive to design reaction paths and associated order parameters that exploit the "soft" nature of these materials to mechanically rather than alchemically morph surfactant assemblies from state to state. Here, we propose a novel method coined "density field thermodynamic integration" (DFTI) that adopts the universality and transferability of alchemical methods while simultaneously exploiting the soft excess interactions between surfactant molecules. DFTI was designed for a rapid quantification of the free energy differences between different metastable structures in soft fluid materials. The DFTI method uses an external field coupled to the local density to mechanically morph the system between metastable states of interest. Here, we explored the capability of the DFTI method to swiftly and accurately calculate free energy differences between states. To this aim, we studied two different coarse-grained lipidic surfactant systems: (i) a fusion stalk and (ii) a worm-like micelle. Our results illustrate that DFTI can provide an efficient, versatile, and rather reliable method to calculate the free energy differences between surfactant assemblies.
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Affiliation(s)
- Laura Josefine Endter
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
| | - Yuliya Smirnova
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany
| | - Herre Jelger Risselada
- Institute for Theoretical Physics, Georg-August University, 37077 Göttingen, Germany.,Leiden Institute of Chemistry (LIC), University of Leiden, 2311 Leiden,The Netherlands.,Chemical Deptartment, Leibniz Institute of Surface Modifications, 04318 Leipzig, Germany
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34
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Feng YH, Zhang XP, Zhao ZQ, Guo XD. Dissipative Particle Dynamics Aided Design of Drug Delivery Systems: A Review. Mol Pharm 2020; 17:1778-1799. [DOI: 10.1021/acs.molpharmaceut.0c00175] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yun Hao Feng
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xiao Peng Zhang
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Ze Qiang Zhao
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xin Dong Guo
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
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35
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Galimzyanov TR, Bashkirov PV, Blank PS, Zimmerberg J, Batishchev OV, Akimov SA. Monolayerwise application of linear elasticity theory well describes strongly deformed lipid membranes and the effect of solvent. SOFT MATTER 2020; 16:1179-1189. [PMID: 31934707 DOI: 10.1039/c9sm02079a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The theory of elasticity of lipid membranes is used widely to describe processes of cell membrane remodeling. Classically, the functional of a membrane's elastic energy is derived under assumption of small deformations; the membrane is considered as an infinitely thin film. This functional is quadratic on membrane surface curvature, with half of the splay modulus as its proportionality coefficient; it is generally applicable for small deformations only. Any validity of this functional for the regime of strong deformations should be verified experimentally. Recently, research using molecular dynamics simulations challenged the validity of this classic, linear model, i.e. the constancy of the splay modulus for strongly bent membranes. Here we demonstrate that the quadratic energy functional still can be applied for calculation of the elastic energy of strongly deformed membranes without introducing higher order terms with additional elastic moduli, but only if applied separately for each lipid monolayer. For cylindrical membranes, both classic and monolayerwise models yield equally accurate results. For cylindrical deformations we experimentally show that the elastic energy of lipid monolayers is additive: a low molecular weight solvent leads to an approximately twofold decrease in the membrane bending stiffness. Accumulation of solvent molecules in the inner monolayer of a membrane cylinder can explain these results, as the solvent partially prevents lipid molecules from splaying there. Thus, the linear theory of elasticity can be expanded through the range from weak to strong deformations-its simplicity and physical transparency describe various membrane phenomena.
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Affiliation(s)
- Timur R Galimzyanov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
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Vasan R, Rudraraju S, Akamatsu M, Garikipati K, Rangamani P. A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction. SOFT MATTER 2020; 16:784-797. [PMID: 31830191 DOI: 10.1039/c9sm01494b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and the range of forces and deflection over which they operate, suggest that the constriction process is functionally mechanical and robust to changes in biological environment. In this study, we used a mechanical model of the lipid bilayer to systematically investigate the influence of location, symmetry constraints, and helical forces on membrane neck constriction. Simulations from our model demonstrated that the energy barriers associated with constriction of a membrane neck are location-dependent. Importantly, if symmetry restrictions are relaxed, then the energy barrier for constriction is dramatically lowered and the membrane buckles at lower values of forcing parameters. Our simulations also show that constriction due to helical proteins further reduces the energy barrier for neck formation when compared to cylindrical proteins. These studies establish that despite different molecular mechanisms of neck formation in cells, the mechanics of constriction naturally leads to a loss of symmetry that can lower the energy barrier to constriction.
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Affiliation(s)
- R Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA.
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Bashkirov PV, Chekashkina KV, Shnyrova AV, Frolov VA. Electrophysiological Methods for Detection of Membrane Leakage and Hemifission by Dynamin 1. Methods Mol Biol 2020; 2159:141-162. [PMID: 32529369 DOI: 10.1007/978-1-0716-0676-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Membrane fusion and fission are indispensable parts of intracellular membrane recycling and transport. Electrophysiological techniques have been instrumental in discovering and studying fusion and fission pores, the key intermediates shared by both processes. In cells, electrical admittance measurements are used to assess in real time the dynamics of the pore conductance, reflecting the nanoscale transformations of the pore, simultaneously with membrane leakage. Here, we described how this technique is adapted to in vitro mechanistic analyses of membrane fission by dynamin 1 (Dyn1), the protein orchestrating membrane fission in endocytosis. We reconstitute the fission reaction using purified Dyn1 and biomimetic lipid membrane nanotubes of defined geometry. We provide a comprehensive protocol describing simultaneous measurements of the ionic conductance through the nanotube lumen and across the nanotube wall, enabling spatiotemporal correlation between the nanotube constriction by Dyn1, leading to fission and membrane leakage. We present examples of "leaky" and "tight" fission reactions, specify the resolution limits of our method, and discuss how our results support the hemi-fission conjecture.
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Affiliation(s)
- Pavel V Bashkirov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia V Chekashkina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Shnyrova
- Department of Biochemistry and Molecular Biology, Biophysics Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
| | - Vadim A Frolov
- Department of Biochemistry and Molecular Biology, Biophysics Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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Espadas J, Pendin D, Bocanegra R, Escalada A, Misticoni G, Trevisan T, Velasco Del Olmo A, Montagna A, Bova S, Ibarra B, Kuzmin PI, Bashkirov PV, Shnyrova AV, Frolov VA, Daga A. Dynamic constriction and fission of endoplasmic reticulum membranes by reticulon. Nat Commun 2019; 10:5327. [PMID: 31757972 PMCID: PMC6876568 DOI: 10.1038/s41467-019-13327-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
The endoplasmic reticulum (ER) is a continuous cell-wide membrane network. Network formation has been associated with proteins producing membrane curvature and fusion, such as reticulons and atlastin. Regulated network fragmentation, occurring in different physiological contexts, is less understood. Here we find that the ER has an embedded fragmentation mechanism based upon the ability of reticulon to produce fission of elongating network branches. In Drosophila, Rtnl1-facilitated fission is counterbalanced by atlastin-driven fusion, with the prevalence of Rtnl1 leading to ER fragmentation. Ectopic expression of Drosophila reticulon in COS-7 cells reveals individual fission events in dynamic ER tubules. Consistently, in vitro analyses show that reticulon produces velocity-dependent constriction of lipid nanotubes leading to stochastic fission via a hemifission mechanism. Fission occurs at elongation rates and pulling force ranges intrinsic to the ER, thus suggesting a principle whereby the dynamic balance between fusion and fission controlling organelle morphology depends on membrane motility.
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Affiliation(s)
- Javier Espadas
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular, Biology, University of the Basque Country, Leioa, 48940, Spain
| | - Diana Pendin
- Scientific Institute, IRCCS E. Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
- Neuroscience Institute, Italian National Research Council (CNR), Padova, Italy
| | - Rebeca Bocanegra
- IMDEA Nanociencia, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Artur Escalada
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular, Biology, University of the Basque Country, Leioa, 48940, Spain
| | - Giulia Misticoni
- Scientific Institute, IRCCS E. Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Tatiana Trevisan
- Scientific Institute, IRCCS E. Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Ariana Velasco Del Olmo
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular, Biology, University of the Basque Country, Leioa, 48940, Spain
| | - Aldo Montagna
- Scientific Institute, IRCCS E. Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Sergio Bova
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Borja Ibarra
- IMDEA Nanociencia, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
- Nanobiotecnología (IMDEA-Nanociencia) Unidad Asociada al Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | - Peter I Kuzmin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anna V Shnyrova
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular, Biology, University of the Basque Country, Leioa, 48940, Spain
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular, Biology, University of the Basque Country, Leioa, 48940, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48013, Spain.
| | - Andrea Daga
- Scientific Institute, IRCCS E. Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy.
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Agrawal A, Ramachandran R. Exploring the links between lipid geometry and mitochondrial fission: Emerging concepts. Mitochondrion 2019; 49:305-313. [DOI: 10.1016/j.mito.2019.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/08/2023]
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Ford MGJ, Chappie JS. The structural biology of the dynamin-related proteins: New insights into a diverse, multitalented family. Traffic 2019; 20:717-740. [PMID: 31298797 DOI: 10.1111/tra.12676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
Abstract
Dynamin-related proteins are multidomain, mechanochemical GTPases that self-assemble and orchestrate a wide array of cellular processes. Over the past decade, structural insights from X-ray crystallography and cryo-electron microscopy have reshaped our mechanistic understanding of these proteins. Here, we provide a historical perspective on these advances that highlights the structural attributes of different dynamin family members and explores how these characteristics affect GTP hydrolysis, conformational coupling and oligomerization. We also discuss a number of lingering challenges remaining in the field that suggest future directions of study.
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Affiliation(s)
- Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York
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Kitamata M, Hanawa-Suetsugu K, Maruyama K, Suetsugu S. Membrane-Deformation Ability of ANKHD1 Is Involved in the Early Endosome Enlargement. iScience 2019; 17:101-118. [PMID: 31255983 PMCID: PMC6606961 DOI: 10.1016/j.isci.2019.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/22/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Ankyrin-repeat domains (ARDs) are conserved in large numbers of proteins. ARDs are composed of various numbers of ankyrin repeats (ANKs). ARDs often adopt curved structures reminiscent of the Bin-Amphiphysin-Rvs (BAR) domain, which is the dimeric scaffold for membrane tubulation. BAR domains sometimes have amphipathic helices for membrane tubulation and vesiculation. However, it is unclear whether ARD-containing proteins exhibit similar membrane deformation properties. We found that the ARD of ANK and KH domain-containing protein 1 (ANKHD1) dimerize and deform membranes into tubules and vesicles. Among 25 ANKs of ANKHD1, the first 15 ANKs can form a dimer and the latter 10 ANKs enable membrane tubulation and vesiculation through an adjacent amphipathic helix and a predicted curved structure with a positively charged surface, analogous to BAR domains. Knockdown and localization of ANKHD1 suggested its involvement in the negative regulation of early endosome enlargement owing to its membrane vesiculation. ANKHD1 is a large protein of 270 kDa, containing 25 ankyrin repeats ANKHD1 generates membrane tubules and vesicles by its ankyrin-repeat domain (ARD). The ARD has an amphipathic helix and a predicted curved structure, like BAR domains ANKHD1 negatively regulates early endosome enlargement by its vesiculation ability
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Affiliation(s)
- Manabu Kitamata
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kohei Maruyama
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Shiro Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
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Velasco-Olmo A, Ormaetxea Gisasola J, Martinez Galvez JM, Vera Lillo J, Shnyrova AV. Combining patch-clamping and fluorescence microscopy for quantitative reconstitution of cellular membrane processes with Giant Suspended Bilayers. Sci Rep 2019; 9:7255. [PMID: 31076583 PMCID: PMC6510758 DOI: 10.1038/s41598-019-43561-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/26/2019] [Indexed: 01/24/2023] Open
Abstract
In vitro reconstitution and microscopic visualization of membrane processes is an indispensable source of information about a cellular function. Here we describe a conceptionally novel free-standing membrane template that facilitates such quantitative reconstitution of membrane remodelling at different scales. The Giant Suspended Bilayers (GSBs) spontaneously swell from lipid lamella reservoir deposited on microspheres. GSBs attached to the reservoir can be prepared from virtually any lipid composition following a fast procedure. Giant unilamellar vesicles can be further obtained by GSB detachment from the microspheres. The reservoir stabilizes GSB during deformations, mechanical micromanipulations, and fluorescence microscopy observations, while GSB-reservoir boundary enables the exchange of small solutes with GSB interior. These unique properties allow studying macro- and nano-scale membrane deformations, adding membrane-active compounds to both sides of GSB membrane and applying patch-clamp based approaches, thus making GSB a versatile tool for reconstitution and quantification of cellular membrane trafficking events.
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Affiliation(s)
- Ariana Velasco-Olmo
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Julene Ormaetxea Gisasola
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Juan Manuel Martinez Galvez
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Javier Vera Lillo
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Anna V Shnyrova
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain.
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Smaczynska-de Rooij II, Marklew CJ, Palmer SE, Allwood EG, Ayscough KR. Mutation of key lysine residues in the Insert B region of the yeast dynamin Vps1 disrupts lipid binding and causes defects in endocytosis. PLoS One 2019; 14:e0215102. [PMID: 31009484 PMCID: PMC6476499 DOI: 10.1371/journal.pone.0215102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The yeast dynamin-like protein Vps1 has roles at multiple stages of membrane trafficking including Golgi to vacuole transport, endosomal recycling, endocytosis and in peroxisomal fission. While the majority of the Vps1 amino acid sequence shows a high level of identity with the classical mammalian dynamins, it does not contain a pleckstrin homology domain (PH domain). The Dyn1 PH domain has been shown to bind to lipids with a preference for PI(4,5)P2 and it is considered central to the function of Dyn1 in endocytosis. The lack of a PH domain in Vps1 has raised questions as to whether the protein can function directly in membrane fusion or fission events. Here we demonstrate that the region Insert B, located in a position equivalent to the dynamin PH domain, is able to bind directly to lipids and that mutation of three lysine residues reduces its capacity to interact with lipids, and in particular with PI(4,5)P2. The Vps1 KKK-AAA mutant shows more diffuse staining but does still show some localization to compartments adjacent to vacuoles and to endocytic sites suggesting that other factors are also involved in its recruitment. This mutant selectively blocks endocytosis, but is functional in other processes tested. While mutant Vps1 can localise to endocytic sites, the mutation results in a significant increase in the lifetime of the endocytic reporter Sla2 and a high proportion of defective scission events. Together our data indicate that the lipid binding capacity of the Insert B region of Vps1 contributes to the ability of the protein to associate with membranes and that its capacity to interact with PI(4,5)P2 is important in facilitating endocytic scission.
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Affiliation(s)
| | | | - Sarah E. Palmer
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Ellen G. Allwood
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (EGA); (KRA)
| | - Kathryn R. Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (EGA); (KRA)
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Donahue ND, Acar H, Wilhelm S. Concepts of nanoparticle cellular uptake, intracellular trafficking, and kinetics in nanomedicine. Adv Drug Deliv Rev 2019; 143:68-96. [PMID: 31022434 DOI: 10.1016/j.addr.2019.04.008] [Citation(s) in RCA: 499] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/14/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022]
Abstract
Nanoparticle-based therapeutics and diagnostics are commonly referred to as nanomedicine and may significantly impact the future of healthcare. However, the clinical translation of these technologies is challenging. One of these challenges is the efficient delivery of nanoparticles to specific cell populations and subcellular targets in the body to elicit desired biological and therapeutic responses. It is critical for researchers to understand the fundamental concepts of how nanoparticles interact with biological systems to predict and control in vivo nanoparticle transport for improved clinical benefit. In this overview article, we review and discuss cellular internalization pathways, summarize the field`s understanding of how nanoparticle physicochemical properties affect cellular interactions, and explore and discuss intracellular nanoparticle trafficking and kinetics. Our overview may provide a valuable resource for researchers and may inspire new studies to expand our current understanding of nanotechnology-biology interactions at cellular and subcellular levels with the goal to improve clinical translation of nanomedicines.
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Affiliation(s)
- Nathan D Donahue
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Handan Acar
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States; Stephenson Cancer Center, Oklahoma City, Oklahoma 73104, United States.
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States; Stephenson Cancer Center, Oklahoma City, Oklahoma 73104, United States.
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Jimah JR, Hinshaw JE. Structural Insights into the Mechanism of Dynamin Superfamily Proteins. Trends Cell Biol 2019; 29:257-273. [DOI: 10.1016/j.tcb.2018.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
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Pannuzzo M, McDargh ZA, Deserno M. The role of scaffold reshaping and disassembly in dynamin driven membrane fission. eLife 2018; 7:39441. [PMID: 30561335 PMCID: PMC6355196 DOI: 10.7554/elife.39441] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022] Open
Abstract
The large GTPase dynamin catalyzes membrane fission in eukaryotic cells, but despite three decades of experimental work, competing and partially conflicting models persist regarding some of its most basic actions. Here we investigate the mechanical and functional consequences of dynamin scaffold shape changes and disassembly with the help of a geometrically and elastically realistic simulation model of helical dynamin-membrane complexes. Beyond changes of radius and pitch, we emphasize the crucial role of a third functional motion: an effective rotation of the filament around its longitudinal axis, which reflects alternate tilting of dynamin’s PH binding domains and creates a membrane torque. We also show that helix elongation impedes fission, hemifission is reached via a small transient pore, and coat disassembly assists fission. Our results have several testable structural consequences and help to reconcile mutual conflicting aspects between the two main present models of dynamin fission—the two-stage and the constrictase model. When cells take up material from their surroundings, they must first transport this cargo across their outer membrane, a flexible sheet of tightly organized fat molecules that act as a barrier to the environment. Cells can achieve this by letting their membrane surround the object, pulling it inwards until it is contained in a pouch that bulges into the cell. This bag is then corded up so it splits off from the outer membrane. The ‘cord’ is a protein called dynamin, which is thought to form a tight spiral around the bag’s neck, closing it over and pinching it away. The structure of dynamin is fairly well known, and yet several theories compete to explain how it may snap the bag off the outer membrane. Here, Pannuzzo et al. have created a computer simulation that faithfully replicates the geometry and the elasticity of the membrane and of dynamin, and used it to test different ways the protein could work. The first test featured simple constriction, where the dynamin spiral contracts around the membrane to pinch it; this only separated the bag from the membrane after implausibly tight constriction. The second test added elongation, with the spiral lengthening as well as reducing its diameter, but this further reduced the ability for the protein to snap off the membrane. The final test combined constriction and rotation, whereby dynamin ‘twirls’ as it presses on the neck of the bag: this succeeded in efficiently severing the membrane once the dynamin spiral disassembled. Indeed, the simulations suggested that dynamin might start to dismantle while it constricts, without compromising its role. In fact, getting rid of excess length as the protein contracts helps to dissolve any remnants of a membrane connection. Defects in dynamin are associated with conditions such as centronuclear myopathy and Charcot‐Marie‐Tooth peripheral neuropathy. Recent research also indicates that the protein is involved in a much wider range of neurological disorders that include Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis. The models created by Pannuzzo et al. are useful tools to understand how dynamin and similar proteins work and sometimes fail.
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Affiliation(s)
- Martina Pannuzzo
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Zachary A McDargh
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, United States
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Deo R, Kushwah MS, Kamerkar SC, Kadam NY, Dar S, Babu K, Srivastava A, Pucadyil TJ. ATP-dependent membrane remodeling links EHD1 functions to endocytic recycling. Nat Commun 2018; 9:5187. [PMID: 30518883 PMCID: PMC6281616 DOI: 10.1038/s41467-018-07586-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 11/02/2018] [Indexed: 01/30/2023] Open
Abstract
Endocytic and recycling pathways generate cargo-laden transport carriers by membrane fission. Classical dynamins, which generate transport carriers during endocytosis, constrict and cause fission of membrane tubes in response to GTP hydrolysis. Relatively, less is known about the ATP-binding Eps15-homology domain-containing protein1 (EHD1), a dynamin family member that functions at the endocytic-recycling compartment. Here, we show using cross complementation assays in C. elegans that EHD1's membrane binding and ATP hydrolysis activities are necessary for endocytic recycling. Further, we show that ATP-bound EHD1 forms membrane-active scaffolds that bulge tubular model membranes. ATP hydrolysis promotes scaffold self-assembly, causing the bulge to extend and thin down intermediate regions on the tube. On tubes below 25 nm in radius, such thinning leads to scission. Molecular dynamics simulations corroborate this scission pathway. Deletion of N-terminal residues causes defects in stable scaffolding, scission and endocytic recycling. Thus, ATP hydrolysis-dependent membrane remodeling links EHD1 functions to endocytic recycling.
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Affiliation(s)
- Raunaq Deo
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Manish S Kushwah
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Sukrut C Kamerkar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Nagesh Y Kadam
- Indian Institute of Science Education and Research, Sector 81, S.A.S Nagar, Mohali, 140306, Punjab, India
| | - Srishti Dar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Kavita Babu
- Indian Institute of Science Education and Research, Sector 81, S.A.S Nagar, Mohali, 140306, Punjab, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Thomas J Pucadyil
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.
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Chand S, Beales P, Claeyssens F, Ciani B. Topography design in model membranes: Where biology meets physics. Exp Biol Med (Maywood) 2018; 244:294-303. [PMID: 30379575 DOI: 10.1177/1535370218809369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
IMPACT STATEMENT Artificial membranes with complex topography aid the understanding of biological processes where membrane geometry plays a key regulatory role. In this review, we highlight how emerging material and engineering technologies have been employed to create minimal models of cell signaling pathways, in vitro. These artificial systems allow life scientists to answer ever more challenging questions with regards to mechanisms in cellular biology. In vitro reconstitution of biology is an area that draws on the expertise and collaboration between biophysicists, material scientists and biologists and has recently generated a number of high impact results, some of which are also discussed in this review.
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Affiliation(s)
- Sarina Chand
- 1 Centre for Membrane Structure and Dynamics, Krebs Institute and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.,2 The Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK
| | - Paul Beales
- 3 School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Frederik Claeyssens
- 2 The Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK
| | - Barbara Ciani
- 1 Centre for Membrane Structure and Dynamics, Krebs Institute and Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
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Ringer K, Riehl J, Müller M, Dewes J, Hoff F, Jacob R. The large GTPase Mx1 binds Kif5B for cargo transport along microtubules. Traffic 2018; 19:947-964. [DOI: 10.1111/tra.12616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Karina Ringer
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling; Philipps University of Marburg; Marburg Germany
| | - Jana Riehl
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
| | - Manuel Müller
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
| | - Jenny Dewes
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
| | - Florian Hoff
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
| | - Ralf Jacob
- Department of Cell Biology and Cell Pathology; Philipps University of Marburg; Marburg Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling; Philipps University of Marburg; Marburg Germany
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Abstract
Dynamin 2 (DNM2) belongs to a family of large GTPases that are well known for mediating membrane fission by oligomerizing at the neck of membrane invaginations. Autosomal dominant mutations in the ubiquitously expressed DNM2 cause 2 discrete neuromuscular diseases: autosomal dominant centronuclear myopathy (ADCNM) and dominant intermediate Charcot-Marie-Tooth neuropathy (CMT). CNM and CMT mutations may affect DNM2 in distinct manners: CNM mutations may cause protein hyperactivity with elevated GTPase and fission activities, while CMT mutations could impair DNM2 lipid binding and activity. DNM2 is also a modifier of the X-linked and autosomal recessive forms of CNM, as DNM2 protein levels are upregulated in animal models and patient muscle samples. Strikingly, reducing DNM2 has been shown to revert muscle phenotypes in preclinical models of CNM. As DNM2 emerges as the key player in CNM pathogenesis, the role(s) of DNM2 in skeletal muscle remains unclear. This review aims to provide insights into potential pathomechanisms related to DNM2-CNM mutations, and discuss exciting outcomes of current and future therapeutic approaches targeting DNM2 hyperactivity.
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Affiliation(s)
- Mo Zhao
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Nika Maani
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - James J Dowling
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Division of Neurology, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Pediatrics, University of Toronto, Toronto, ON, M5G 1X8, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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