1
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Sambre P, Ho JCS, Parikh AN. Intravesicular Solute Delivery and Surface Area Regulation in Giant Unilamellar Vesicles Driven by Cycles of Osmotic Stresses. J Am Chem Soc 2024; 146:3250-3261. [PMID: 38266489 PMCID: PMC10859933 DOI: 10.1021/jacs.3c11679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
Phospholipid bilayers are dynamic cellular components that undergo constant changes in their topology, facilitating a broad diversity of physiological functions including endo- and exocytosis, cell division, and intracellular trafficking. These shape transformations consume energy, supplied invariably by the activity of proteins. Here, we show that cycles of oppositely directed osmotic stresses─unassisted by any protein activity─can induce well-defined remodeling of giant unilamellar vesicles, minimally recapitulating the phenomenologies of surface area homeostasis and macropinocytosis. We find that a stress cycle consisting of deflationary hypertonic stress followed by an inflationary hypotonic one prompts an elaborate sequence of membrane shape changes ultimately transporting molecular cargo from the outside into the intravesicular milieu. The initial osmotic deflation produces microscopic spherical invaginations. During the subsequent inflation, the first subpopulation contributes area to the swelling membrane, thereby providing a means for surface area regulation and tensional homeostasis. The second subpopulation vesiculates into the lumens of the mother vesicles, producing pinocytic vesicles. Remarkably, the gradients of solute concentrations between the GUV and the daughter pinocytic vesicles create cascades of water current, inducing pulsatory transient poration that enable solute exchange between the buds and the GUV interior. This results in an efficient water-flux-mediated delivery of molecular cargo across the membrane boundary. Our findings suggest a primitive physical mechanism for communication and transport across protocellular compartments driven only by osmotic stresses. They also suggest plausible physical routes for intravesicular, and possibly intracellular, delivery of ions, solutes, and molecular cargo stimulated simply by cycles of osmotic currents of water.
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Affiliation(s)
- Pallavi
D. Sambre
- Department
of Materials Science and Engineering, University
of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - James C. S. Ho
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore
- Institute
for Digital Molecular Analytics and Science, Nanyang Technological University, 60 Nanyang Drive, 637551Singapore
| | - Atul N. Parikh
- Department
of Materials Science and Engineering, University
of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Singapore
Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 59 Nanyang Drive, 636921 Singapore
- Institute
for Digital Molecular Analytics and Science, Nanyang Technological University, 60 Nanyang Drive, 637551Singapore
- Department
of Biomedical Engineering, University of
California, Davis, One Shields Avenue, Davis, California 95616, United States
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2
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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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3
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Aftahy K, Arrasate P, Bashkirov PV, Kuzmin PI, Maurizot V, Huc I, Frolov VA. Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers. J Am Chem Soc 2023; 145:25150-25159. [PMID: 37948300 PMCID: PMC10682987 DOI: 10.1021/jacs.3c05753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.
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Affiliation(s)
- Kathrin Aftahy
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Pedro Arrasate
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
| | - Pavel V. Bashkirov
- Research
Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Petr I. Kuzmin
- A.N.
Frumkin Institute of Physical Chemistry and Electrochemistry, Moscow 119071, Russia
| | - Victor Maurizot
- Univ. Bordeaux,
CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Pessac 33600, France
| | - Ivan Huc
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Munich 81377, Germany
| | - Vadim A. Frolov
- Biofisika
Institute (CSIC, UPV/EHU), University of
the Basque Country, Leioa 48940, Spain
- Department
of Biochemistry and Molecular Biology, University
of the Basque Country, Leioa 48940, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48009, Spain
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4
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Su R, Wang S, McDargh Z, O'Shaughnessy B. Three membrane fusion pore families determine the pathway to pore dilation. Biophys J 2023; 122:3986-3998. [PMID: 37644721 PMCID: PMC10560699 DOI: 10.1016/j.bpj.2023.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/19/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
During exocytosis secretory vesicles fuse with a target membrane and release neurotransmitters, hormones, or other bioactive molecules through a membrane fusion pore. The initially small pore may subsequently dilate for full contents release, as commonly observed in amperometric traces. The size, shape, and evolution of the pore is critical to the course of contents release, but exact fusion pore solutions accounting for membrane tension and bending energy constraints have not been available. Here, we obtained exact solutions for fusion pores between two membranes. We find three families: a narrow pore, a wide pore, and an intermediate tether-like pore. For high tensions these are close to the catenoidal and tether solutions recently reported for freely hinged membrane boundaries. We suggest membrane fusion initially generates a stable narrow pore, and the dilation pathway is a transition to the stable wide pore family. The unstable intermediate pore is the transition state that sets the energy barrier for this dilation pathway. Pore dilation is mechanosensitive, as the energy barrier is lowered by increased membrane tension. Finally, we study fusion pores in nanodiscs, powerful systems for the study of individual pores. We show that nanodiscs stabilize fusion pores by locking them into the narrow pore family.
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Affiliation(s)
- Rui Su
- Department of Chemical Engineering, Columbia University, New York City, New York
| | - Shuyuan Wang
- Department of Chemical Engineering, Columbia University, New York City, New York; Department of Physics, Columbia University, New York City, New York
| | - Zachary McDargh
- Department of Chemical Engineering, Columbia University, New York City, New York
| | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York City, New York.
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5
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Santiago JA, Monroy F. Inhomogeneous Canham-Helfrich Abscission in Catenoid Necks under Critical Membrane Mosaicity. MEMBRANES 2023; 13:796. [PMID: 37755218 PMCID: PMC10534449 DOI: 10.3390/membranes13090796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023]
Abstract
The mechanical effects of membrane compositional inhomogeneities are analyzed in a process analogous to neck formation in cellular membranes. We cast on the Canham-Helfrich model of fluid membranes with both the spontaneous curvature and the surface tension being non-homogeneous functions along the cell membrane. The inhomogeneous distribution of necking forces is determined by the equilibrium mechanical equations and the boundary conditions as considered in the axisymmetric setting compatible with the necking process. To establish the role played by mechanical inhomogeneity, we focus on the catenoid, a surface of zero mean curvature. Analytic solutions are shown to exist for the spontaneous curvature and the constrictive forces in terms of the border radii. Our theoretical analysis shows that the inhomogeneous distribution of spontaneous curvature in a mosaic-like neck constrictional forces potentially contributes to the membrane scission under minimized work in living cells.
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Affiliation(s)
- José Antonio Santiago
- Departamento de Matemáticas Aplicadas y Sistemas, Universidad Autónoma Metropolitana Cuajimalpa, Vasco de Quiroga 4871, Ciudad de México 05384, Mexico
- Departamento de Química Física, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
- Translational Biophysics, Institute for Biomedical Research, Hospital Doce de Octubre (imas12), Av. Andalucía s/n, 28041 Madrid, Spain
| | - Francisco Monroy
- Departamento de Química Física, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain;
- Translational Biophysics, Institute for Biomedical Research, Hospital Doce de Octubre (imas12), Av. Andalucía s/n, 28041 Madrid, Spain
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6
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Yu Y, Yoshimura SH. Self-assembly of CIP4 drives actin-mediated asymmetric pit-closing in clathrin-mediated endocytosis. Nat Commun 2023; 14:4602. [PMID: 37528083 PMCID: PMC10393992 DOI: 10.1038/s41467-023-40390-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 07/23/2023] [Indexed: 08/03/2023] Open
Abstract
Clathrin-mediated endocytosis is pivotal to signal transduction pathways between the extracellular environment and the intracellular space. Evidence from live-cell imaging and super-resolution microscopy of mammalian cells suggests an asymmetric distribution of actin fibres near the clathrin-coated pit, which induces asymmetric pit-closing rather than radial constriction. However, detailed molecular mechanisms of this 'asymmetricity' remain elusive. Herein, we used high-speed atomic force microscopy to demonstrate that CIP4, a multi-domain protein with a classic F-BAR domain and intrinsically disordered regions, is necessary for asymmetric pit-closing. Strong self-assembly of CIP4 via intrinsically disordered regions, together with stereospecific interactions with the curved membrane and actin-regulating proteins, generates a small actin-rich environment near the pit, which deforms the membrane and closes the pit. Our results provide mechanistic insights into how disordered and structured domain collaboration promotes spatio-temporal actin polymerisation near the plasma membrane.
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Affiliation(s)
- Yiming Yu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
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7
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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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8
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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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9
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Rice A, Zimmerberg J, Pastor RW. Initiation and evolution of pores formed by influenza fusion peptides probed by lysolipid inclusion. Biophys J 2023; 122:1018-1032. [PMID: 36575795 PMCID: PMC10111278 DOI: 10.1016/j.bpj.2022.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The fusion peptide (FP) domain is necessary for the fusogenic activity of spike proteins in a variety of enveloped viruses, allowing the virus to infect the host cell, and is the only part of the protein that interacts directly with the target membrane lipid tails during fusion. There are consistent findings of poration by this domain in experimental model membrane systems, and, in certain conditions, the isolated FPs can generate pores. Here, we use molecular dynamics simulations to investigate the specifics of how these FP-induced pores form in membranes with different compositions of lysolipid and POPC. The simulations show that pores form spontaneously at high lysolipid concentrations via hybrid intermediates, where FP aggregates in the cis leaflet tilt to form a funnel-like structure that spans the leaflet and locally reduces the hydrophobic thickness that must be traversed by water to form a pore. By restraining a single FP within an FP aggregate to this tilted conformation, pores can be formed in lower-lysolipid-content membranes, including pure POPC, on the 100-ns timescale, much more rapidly than in unbiased simulations in bilayers with the same composition. The pore formation pathway is similar to the spontaneous formation in high lysolipid concentrations. Depending on the membrane composition, the pores can be metastable (as seen in POPC) or lead to membrane rupture.
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Affiliation(s)
- Amy Rice
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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10
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Khurana H, Baratam K, Bhattacharyya S, Srivastava A, Pucadyil TJ. Mechanistic analysis of a novel membrane-interacting variable loop in the pleckstrin-homology domain critical for dynamin function. Proc Natl Acad Sci U S A 2023; 120:e2215250120. [PMID: 36888655 PMCID: PMC10089193 DOI: 10.1073/pnas.2215250120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023] Open
Abstract
Classical dynamins are best understood for their ability to generate vesicles by membrane fission. During clathrin-mediated endocytosis (CME), dynamin is recruited to the membrane through multivalent protein and lipid interactions between its proline-rich domain (PRD) with SRC Homology 3 (SH3) domains in endocytic proteins and its pleckstrin-homology domain (PHD) with membrane lipids. Variable loops (VL) in the PHD bind lipids and partially insert into the membrane thereby anchoring the PHD to the membrane. Recent molecular dynamics (MD) simulations reveal a novel VL4 that interacts with the membrane. Importantly, a missense mutation that reduces VL4 hydrophobicity is linked to an autosomal dominant form of Charcot-Marie-Tooth (CMT) neuropathy. We analyzed the orientation and function of the VL4 to mechanistically link data from simulations with the CMT neuropathy. Structural modeling of PHDs in the cryo-electron microscopy (cryo-EM) cryoEM map of the membrane-bound dynamin polymer confirms VL4 as a membrane-interacting loop. In assays that rely solely on lipid-based membrane recruitment, VL4 mutants with reduced hydrophobicity showed an acute membrane curvature-dependent binding and a catalytic defect in fission. Remarkably, in assays that mimic a physiological multivalent lipid- and protein-based recruitment, VL4 mutants were completely defective in fission across a range of membrane curvatures. Importantly, expression of these mutants in cells inhibited CME, consistent with the autosomal dominant phenotype associated with the CMT neuropathy. Together, our results emphasize the significance of finely tuned lipid and protein interactions for efficient dynamin function.
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Affiliation(s)
- Himani Khurana
- Indian Institute of Science Education and Research, Pune411008, India
| | | | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru560012, India
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11
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Kalutskii MA, Galimzyanov TR, Pinigin KV. Determination of elastic parameters of lipid membranes from simulation under varied external pressure. Phys Rev E 2023; 107:024414. [PMID: 36932616 DOI: 10.1103/physreve.107.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Many cellular processes such as endocytosis, exocytosis, and vesicle trafficking involve membrane deformations, which can be analyzed in the framework of the elastic theories of lipid membranes. These models operate with phenomenological elastic parameters. A connection between these parameters and the internal structure of lipid membranes can be provided by three-dimensional (3D) elastic theories. Considering a membrane as a 3D layer, Campelo et al. [F. Campelo et al., Adv. Colloid Interface Sci. 208, 25 (2014)10.1016/j.cis.2014.01.018] developed a theoretical basis for the calculation of elastic parameters. In this work we generalize and improve this approach by considering a more general condition of global incompressibility instead of local incompressibility. Crucially, we find an important correction to the theory of Campelo et al., which if not taken into account leads to a significant miscalculation of elastic parameters. With the total volume conservation taken into account, we derive an expression for the local Poisson's ratio, which determines how the local volume changes upon stretching and permits a more precise determination of elastic parameters. Also, we substantially simplify the procedure by calculating the derivatives of the moments of the local tension with respect to stretching instead of calculating the local stretching modulus. We obtain a relation between the Gaussian curvature modulus as a function of stretching and the bending modulus, showing that these two elastic parameters are not independent, as was previously assumed. The proposed algorithm is applied to membranes composed of pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and their mixture. The following elastic parameters of these systems are obtained: the monolayer bending and stretching moduli, spontaneous curvature, neutral surface position, and local Poisson's ratio. It is shown that the bending modulus of the DPPC/DOPC mixture follows a more complex trend than predicted by the classical Reuss averaging, which is often employed in theoretical frameworks.
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Affiliation(s)
- Maksim A Kalutskii
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology "MISiS," 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Konstantin V Pinigin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, Moscow 119071, Russia
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12
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Rice A, Haldar S, Wang E, Blank PS, Akimov SA, Galimzyanov TR, Pastor RW, Zimmerberg J. Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration. Nat Commun 2022; 13:7336. [PMID: 36470871 PMCID: PMC9722698 DOI: 10.1038/s41467-022-34576-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/28/2022] [Indexed: 12/07/2022] Open
Abstract
To infect, enveloped viruses employ spike protein, spearheaded by its amphipathic fusion peptide (FP), that upon activation extends out from the viral surface to embed into the target cellular membrane. Here we report that synthesized influenza virus FPs are membrane active, generating pores in giant unilamellar vesicles (GUV), and thus potentially explain both influenza virus' hemolytic activity and the liposome poration seen in cryo-electron tomography. Experimentally, FPs are heterogeneously distributed on the GUV at the time of poration. Consistent with this heterogeneous distribution, molecular dynamics (MD) simulations of asymmetric bilayers with different numbers of FPs in one leaflet show FP aggregation. At the center of FP aggregates, a profound change in the membrane structure results in thinning, higher water permeability, and curvature. Ultimately, a hybrid bilayer nanodomain forms with one lipidic leaflet and one peptidic leaflet. Membrane elastic theory predicts a reduced barrier to water pore formation when even a dimer of FPs thins the membrane as above, and the FPs of that dimer tilt, to continue the leaflet bending initiated by the hydrophobic mismatch between the FP dimer and the surrounding lipid.
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Affiliation(s)
- Amy Rice
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Sourav Haldar
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA ,grid.418363.b0000 0004 0506 6543Present Address: Division of Virus Research and Therapeutics, CSIR-Central Drug Research Institute, Lucknow, UP India
| | - Eric Wang
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Paul S. Blank
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Sergey A. Akimov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Timur R. Galimzyanov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia ,grid.35043.310000 0001 0010 3972National University of Science and Technology “MISiS”, 4 Leninskiy Prospect, Moscow, Russia
| | - Richard W. Pastor
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Joshua Zimmerberg
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
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13
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Molotkovsky RJ, Kuzmin PI. Fusion of Peroxisome and Lipid Droplet Membranes: Expansion of a π-Shaped Structure. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Gómez-Oca R, Edelweiss E, Djeddi S, Gerbier M, Massana-Muñoz X, Oulad-Abdelghani M, Crucifix C, Spiegelhalter C, Messaddeq N, Poussin-Courmontagne P, Koebel P, Cowling BS, Laporte J. Differential impact of ubiquitous and muscle dynamin 2 isoforms in muscle physiology and centronuclear myopathy. Nat Commun 2022; 13:6849. [PMID: 36369230 PMCID: PMC9652393 DOI: 10.1038/s41467-022-34490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Dynamin 2 mechanoenzyme is a key regulator of membrane remodeling and gain-of-function mutations in its gene cause centronuclear myopathies. Here, we investigate the functions of dynamin 2 isoforms and their associated phenotypes and, specifically, the ubiquitous and muscle-specific dynamin 2 isoforms expressed in skeletal muscle. In cell-based assays, we show that a centronuclear myopathy-related mutation in the ubiquitous but not the muscle-specific dynamin 2 isoform causes increased membrane fission. In vivo, overexpressing the ubiquitous dynamin 2 isoform correlates with severe forms of centronuclear myopathy, while overexpressing the muscle-specific isoform leads to hallmarks seen in milder cases of the disease. Previous mouse studies suggested that reduction of the total dynamin 2 pool could be therapeutic for centronuclear myopathies. Here, dynamin 2 splice switching from muscle-specific to ubiquitous dynamin 2 aggravated the phenotype of a severe X-linked form of centronuclear myopathy caused by loss-of-function of the MTM1 phosphatase, supporting the importance of targeting the ubiquitous isoform for efficient therapy in muscle. Our results highlight that the ubiquitous and not the muscle-specific dynamin 2 isoform is the main modifier contributing to centronuclear myopathy pathology.
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Affiliation(s)
- Raquel Gómez-Oca
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France ,Dynacure, Illkirch, France
| | - Evelina Edelweiss
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Sarah Djeddi
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | | | - Xènia Massana-Muñoz
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Mustapha Oulad-Abdelghani
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Corinne Crucifix
- grid.420255.40000 0004 0638 2716Integrated Structural Biology platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Coralie Spiegelhalter
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Nadia Messaddeq
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Pierre Poussin-Courmontagne
- grid.420255.40000 0004 0638 2716Integrated Structural Biology platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Pascale Koebel
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | | | - Jocelyn Laporte
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
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15
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Solinger JA, Spang A. Sorting of cargo in the tubular endosomal network. Bioessays 2022; 44:e2200158. [DOI: 10.1002/bies.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Anne Spang
- Biozentrum University of Basel Basel Switzerland
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16
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Larijani B, Pytowski L, Vaux DJ. The enigma of phosphoinositides and their derivatives: Their role in regulation of subcellular compartment morphology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1864:183780. [PMID: 34547252 DOI: 10.1016/j.bbamem.2021.183780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022]
Abstract
The general segregation of a molecular class, lipids, from the pathways of cellular communication, via endo-membranes, has resulted in the over-simplification and misconceptions in deciphering cell signalling mechanisms. Mechanisms in signal transduction and protein activation require targeting of proteins to membranous compartments with a specific localised morphology and dynamics that are dependent on their lipid composition. Many posttranslational events define cellular behaviours and without the active role of membranous compartments these events lead to various dysregulations of the signalling pathways. We summarise the key findings, using tools such as the rapalogue dimerisation, in the structural roles and signalling of the inter-related phosphoinositide lipids and their derivative, diacylglycerol, in the regulation of nuclear envelope biogenesis and other subcellular compartments such as the nucleoplasmic reticulum.
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Affiliation(s)
- Banafshé Larijani
- Centre for Therapeutic Innovation & Cell Biophysics Laboratory, Department of Pharmacy and Pharmacology & Department of Physics, University of Bath, Bath BA2 7AY, UK.
| | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David J Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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17
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A large-scale nanoscopy and biochemistry analysis of postsynaptic dendritic spines. Nat Neurosci 2021; 24:1151-1162. [PMID: 34168338 DOI: 10.1038/s41593-021-00874-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
Dendritic spines, the postsynaptic compartments of excitatory neurotransmission, have different shapes classified from 'stubby' to 'mushroom-like'. Whereas mushroom spines are essential for adult brain function, stubby spines disappear during brain maturation. It is still unclear whether and how they differ in protein composition. To address this, we combined electron microscopy and quantitative biochemistry with super-resolution microscopy to annotate more than 47,000 spines for more than 100 synaptic targets. Surprisingly, mushroom and stubby spines have similar average protein copy numbers and topologies. However, an analysis of the correlation of each protein to the postsynaptic density mass, used as a marker of synaptic strength, showed substantially more significant results for the mushroom spines. Secretion and trafficking proteins correlated particularly poorly to the strength of stubby spines. This suggests that stubby spines are less likely to adequately respond to dynamic changes in synaptic transmission than mushroom spines, which possibly explains their loss during brain maturation.
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18
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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: 21] [Impact Index Per Article: 7.0] [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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19
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Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor. Proc Natl Acad Sci U S A 2021; 118:2101144118. [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Dynamin is a protein that is a central player in endocytosis, a process that mediates the entry of diverse particles into cells, from nutrients to viruses. Dynamin’s primary activity is to use guanosine triphosphate as fuel to constrict and cut membrane tubes. Key quantitative aspects of its function remain yet unclear. In this work, we determine the strength of an individual dynamin motor. Then, by building a detailed computational model resolving individual motors, we demonstrate that dynamin produces sufficient force to tightly constrict a membrane tube when most of its motors are simultaneously cooperating. Hence, we quantitatively validate the prevailing constriction-by-ratchet model for nature’s strongest torque-generating motor: the dynamin “nanomuscle.” 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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20
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Ivchenkov DV, Kuzmin PI, Galimzyanov TR, Shnyrova AV, Bashkirov PV, Frolov VA. Nonlinear material and ionic transport through membrane nanotubes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183677. [PMID: 34118214 DOI: 10.1016/j.bbamem.2021.183677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
Membrane nanotubes (NTs) and their networks play an important role in intracellular membrane transport and intercellular communications. The transport characteristics of the NT lumen resemble those of conventional solid-state nanopores. However, unlike the rigid pores, the soft membrane wall of the NT can be deformed by forces driving the transport through the NT lumen. This intrinsic coupling between the NT geometry and transport properties remains poorly explored. Using synchronized fluorescence microscopy and conductance measurements, we revealed that the NT shape was changed by both electric and hydrostatic forces driving the ionic and solute fluxes through the NT lumen. Far from the shape instability, the strength of the force effect is determined by the lateral membrane tension and is scaled with membrane elasticity so that the NT can be operated as a linear elastic sensor. Near shape instabilities, the transport forces triggered large-scale shape transformations, both stochastic and periodic. The periodic oscillations were coupled to a vesicle passage along the NT axis, resembling peristaltic transport. The oscillations were parametrically controlled by the electric field, making NT a highly nonlinear nanofluidic circuitry element with biological and technological implications.
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Affiliation(s)
- D V Ivchenkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Institutskiy lane 9, Dolgoprudnyy, Moskow region 141700, Russia
| | - P I Kuzmin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - T R Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - A V Shnyrova
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain
| | - P V Bashkirov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia; Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Institutskiy lane 9, Dolgoprudnyy, Moskow region 141700, Russia.
| | - V A Frolov
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country, barrio Sarriena s/n, 48940 Leioa, Spain; Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 6 solairua, 48013 Bilbao, Spain.
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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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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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23
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Pinigin KV, Kuzmin PI, Akimov SA, Galimzyanov TR. Additional contributions to elastic energy of lipid membranes: Tilt-curvature coupling and curvature gradient. Phys Rev E 2020; 102:042406. [PMID: 33212684 DOI: 10.1103/physreve.102.042406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/09/2020] [Indexed: 11/07/2022]
Abstract
Lipid bilayer membranes under biologically relevant conditions are flexible thin laterally fluid films consisting of two unimolecular layers (monolayers) each about 2 nm thick. On spatial scales much larger than the bilayer thickness, the membrane elasticity is well determined by its shape. The classical Helfrich theory considers the membrane as an elastic two-dimensional (2D) film, which has no particular internal structure. However, various local membrane heterogeneities can result in a lipids tilt relative to the membrane surface normal. On the basis of the classical elasticity theory of 3D bodies, Hamm and Kozlov [Eur. Phys. J. E 3, 323 (2000)10.1007/s101890070003] derived the most general energy functional, taking into account the tilt and lipid monolayer curvature. Recently, Terzi and Deserno [J. Chem. Phys. 147, 084702 (2017)10.1063/1.4990404] showed that Hamm and Kozlov's derivation was incomplete because the tilt-curvature coupling term had been missed. However, the energy functional derived by Terzi and Deserno appeared to be unstable, thereby being invalid for applications that require minimizations of the overall energy of deformations. Here, we derive a stable elastic energy functional, showing that the squared gradient of the curvature was missed in both of these works. This change in the energy functional arises from a more accurate consideration of the transverse shear deformation terms and their influence on the membrane stability. We also consider the influence of the prestress terms on the stability of the energy functional, and we show that it should be considered small and the effective Gaussian curvature should be neglected because of the stability requirements. We further generalize the theory, including the stretching-compressing deformation modes, and we provide the geometrical interpretation of the terms that were previously missed by Hamm and Kozlov. The physical consequences of the new terms are analyzed in the case of a membrane-mediated interaction of two amphipathic peptides located in the same monolayer. We also provide the expression for director fluctuations, comparing it with that obtained by Terzi and Deserno.
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Affiliation(s)
- Konstantin V Pinigin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
| | - Peter I Kuzmin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
| | - Sergey A Akimov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
| | - Timur R Galimzyanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy prospekt, Moscow 119071, Russia
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24
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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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25
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Martinez Galvez JM, Garcia-Hernando M, Benito-Lopez F, Basabe-Desmonts L, Shnyrova AV. Microfluidic chip with pillar arrays for controlled production and observation of lipid membrane nanotubes. LAB ON A CHIP 2020; 20:2748-2755. [PMID: 32602490 DOI: 10.1039/d0lc00451k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Lipid membrane nanotubes (NTs) are a widespread template for in vitro studies of cellular processes happening at high membrane curvature. Traditionally NTs are manufactured one by one, using sophisticated membrane micromanipulations, while simplified methods for controlled batch production of NTs are in growing demand. Here we propose a lab-on-a-chip (LOC) approach to the simultaneous formation of multiple NTs with length and radius controlled by the chip design. The NTs form upon rolling silica microbeads covered by lipid lamellas over the pillars of a polymer micropillar array. The array's design and surface chemistry set the geometry of the resulting free-standing NTs. The integration of the array inside a microfluidic chamber further enables fast and turbulence-free addition of components, such as proteins, to multiple preformed NTs. This LOC approach to NT production is compatible with the use of high power objectives of a fluorescence microscope, making real-time quantification of the different modes of the protein activity in a single experiment possible.
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Affiliation(s)
- Juan Manuel Martinez Galvez
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain.
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26
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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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27
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Bonnycastle K, Davenport EC, Cousin MA. Presynaptic dysfunction in neurodevelopmental disorders: Insights from the synaptic vesicle life cycle. J Neurochem 2020; 157:179-207. [PMID: 32378740 DOI: 10.1111/jnc.15035] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
The activity-dependent fusion, retrieval and recycling of synaptic vesicles is essential for the maintenance of neurotransmission. Until relatively recently it was believed that most mutations in genes that were essential for this process would be incompatible with life, because of this fundamental role. However, an ever-expanding number of mutations in this very cohort of genes are being identified in individuals with neurodevelopmental disorders, including autism, intellectual disability and epilepsy. This article will summarize the current state of knowledge linking mutations in presynaptic genes to neurodevelopmental disorders by sequentially covering the various stages of the synaptic vesicle life cycle. It will also discuss how perturbations of specific stages within this recycling process could translate into human disease. Finally, it will also provide perspectives on the potential for future therapy that are targeted to presynaptic function.
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Affiliation(s)
- Katherine Bonnycastle
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Elizabeth C Davenport
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
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28
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Roy D, Steinkühler J, Zhao Z, Lipowsky R, Dimova R. Mechanical Tension of Biomembranes Can Be Measured by Super Resolution (STED) Microscopy of Force-Induced Nanotubes. NANO LETTERS 2020; 20:3185-3191. [PMID: 32320255 PMCID: PMC7304919 DOI: 10.1021/acs.nanolett.9b05232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Indexed: 05/26/2023]
Abstract
Membrane tension modulates the morphology of plasma-membrane tubular protrusions in cells but is difficult to measure. Here, we propose to use microscopy imaging to assess the membrane tension. We report direct measurement of membrane nanotube diameters with unprecedented resolution using stimulated emission depletion (STED) microscopy. For this purpose, we integrated an optical tweezers setup in a commercial microscope equipped for STED imaging and established micropipette aspiration of giant vesicles. Membrane nanotubes were pulled from the vesicles at specific membrane tension imposed by the aspiration pipet. Tube diameters calculated from the applied tension using the membrane curvature elasticity model are in excellent agreement with data measured directly with STED. Our approach can be extended to cellular membranes and will then allow us to estimate the mechanical membrane tension within the force-induced nanotubes.
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29
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Ermakov YA, Sokolov VS, Akimov SA, Batishchev OV. Physicochemical and Electrochemical Aspects of the Functioning of Biological Membranes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420030085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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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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31
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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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32
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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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33
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Carravilla P, Darré L, Oar-Arteta IR, Vesga AG, Rujas E, de Las Heras-Martínez G, Domene C, Nieva JL, Requejo-Isidro J. The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane. Biophys J 2019; 118:44-56. [PMID: 31787208 DOI: 10.1016/j.bpj.2019.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/15/2023] Open
Abstract
Efficient engagement with the envelope glycoprotein membrane-proximal external region (MPER) results in robust blocking of viral infection by a class of broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV). Developing an accommodation surface that engages with the viral lipid envelope appears to correlate with the neutralizing potency displayed by these bnAbs. The nature of the interactions established between the antibody and the lipid is nonetheless a matter of debate, with some authors arguing that anti-MPER specificity arises only under pathological conditions in autoantibodies endowed with stereospecific binding sites for phospholipids. However, bnAb-lipid interactions are often studied in systems that do not fully preserve the biophysical properties of lipid bilayers, and therefore, questions on binding specificity and the effect of collective membrane properties on the interaction are still open. Here, to evaluate the specificity of lipid interactions of an anti-MPER bnAb (4E10) in an intact membrane context, we determine quantitatively its association with lipid bilayers by means of scanning fluorescence correlation spectroscopy and all-atom molecular dynamic simulations. Our data support that 4E10 establishes electrostatic and hydrophobic interactions with the viral membrane surface and that the collective physical properties of the lipid bilayer influence 4E10 dynamics therein. We conclude that establishment of peripheral, nonspecific electrostatic interactions with the viral membrane through accommodation surfaces may assist high-affinity binding of HIV-1 MPER epitope at membrane interfaces. These findings highlight the importance of considering antibody-lipid interactions in the design of antibody-based anti-HIV strategies.
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Affiliation(s)
- Pablo Carravilla
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain; Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Leonardo Darré
- Functional Genomics Laboratory & Biomolecular Simulations Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Itziar R Oar-Arteta
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Arturo G Vesga
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Edurne Rujas
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | | | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath, United Kingdom; Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jose L Nieva
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - Jose Requejo-Isidro
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Spain; Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Unidad de Nanobiotecnología, CNB-CSIC-IMDEA Nanociencia Associated Unit, Madrid, Spain.
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34
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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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35
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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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36
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Hilgemann DW, Lin MJ, Fine M, Deisl C. On the existence of endocytosis driven by membrane phase separations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183007. [PMID: 31202864 DOI: 10.1016/j.bbamem.2019.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 01/15/2023]
Abstract
Large endocytic responses can occur rapidly in diverse cell types without dynamins, clathrin, or actin remodeling. Our experiments suggest that membrane phase separations are crucial with more ordered plasma membrane domains being internalized. Not only do these endocytic processes rely on coalescence of membrane domains, they are promoted by participation of membrane proteins in such domains, one important regulatory influence being palmitoylation. Membrane actin cytoskeleton in general resists membrane phase transitions, and its remodeling may play many roles. Besides membrane 'caging' and 'pinching' roles, typically ascribed to clathrin and dynamins, cytoskeleton remodeling may modify local membrane tension and buckling, as well as the presence and location of actin- and tension-free membrane patches. Endocytosis that depends on membrane phase separations becomes activated in metabolic stress and in response to Ca and PI3 kinase signaling. Internalized membrane traffics normally, and the secretory pathway eventually resupplies membrane to the plasmalemma or directs internalized membrane to other locations, including the extracellular space as exosomes. We describe here that endocytosis driven by membrane phase transitions is regulated by the same signaling mechanisms that regulate macropinocytosis, and it may play diverse roles in cells from nutrient assimilation to membrane recycling, cell migration, and the initiation of quiescent or hibernating cell states. Membrane ordering and phase separations have been shown to promote endocytosis in diverse cell types, including fibroblasts, myocytes, glial cells, and immune cells. We propose that clathrin/dynamin-independent endocytosis represents a continuum of related mechanisms with variable but universal dependence on membrane ordering and actin remodeling. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Donald W Hilgemann
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA.
| | - Mei-Jung Lin
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
| | - Michael Fine
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
| | - Christine Deisl
- University of Texas Southwestern Medical Center, Department of Physiology, 5323 Harry Hines Boulevard, Dallas, TX 75235-9040, USA
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37
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Abstract
Dynamin proteins assemble into characteristic helical structures around necks of clathrin-coated membrane buds. Hydrolysis of dynamin-bound GTP results in both fission of the membrane neck and partial disruption of the dynamin oligomer. Imaging by atomic force microscopy reveals that, on GTP hydrolysis, dynamin oligomers undergo a dynamic remodeling and lose their distinctive helical shape. While breakup of the dynamin helix is a critical stage in clathrin-mediated endocytosis, the mechanism for this remodeling of the oligomer has not been resolved. In this paper, we formulate an analytical, elasticity-based model for the reshaping and disassembly of the dynamin scaffold. We predict that the shape of the oligomer is modulated by the orientation of dynamin's pleckstrin homology (PH) domain relative to the underlying membrane. Our results indicate that tilt of the PH domain drives deformation and fragmentation of the oligomer, in agreement with experimental observations. This model motivated the introduction of the tilted helix: a curve that maintains a fixed angle between its normal and the normal of the embedding surface. Our findings highlight the importance of tilt as a key regulator of size and morphology of membrane-bound oligomers.
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38
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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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39
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Dimova R. Giant Vesicles and Their Use in Assays for Assessing Membrane Phase State, Curvature, Mechanics, and Electrical Properties. Annu Rev Biophys 2019; 48:93-119. [DOI: 10.1146/annurev-biophys-052118-115342] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Giant unilamellar vesicles represent a promising and extremely useful model biomembrane system for systematic measurements of mechanical, thermodynamic, electrical, and rheological properties of lipid bilayers as a function of membrane composition, surrounding media, and temperature. The most important advantage of giant vesicles over other model membrane systems is that the membrane responses to external factors such as ions, (macro)molecules, hydrodynamic flows, or electromagnetic fields can be directly observed under the microscope. Here, we briefly review approaches for giant vesicle preparation and describe several assays used for deducing the membrane phase state and measuring a number of material properties, with further emphasis on membrane reshaping and curvature.
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Affiliation(s)
- Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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40
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Kheyfets B, Galimzyanov T, Mukhin S. Lipid lateral self-diffusion drop at liquid-gel phase transition. Phys Rev E 2019; 99:012414. [PMID: 30780230 DOI: 10.1103/physreve.99.012414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/06/2022]
Abstract
A drop of lipid lateral self-diffusion coefficient at the liquid-gel phase transition in lipid membranes is calculated. So far this drop was missing theoretical description. Our microscopic model captures so-called subdiffusion regime, which takes place on 1 ps-100 ns timescale and reveals a jump of self-diffusion coefficient. Calculation of the jump is based on our recent study of liquid-gel phase transition. Subdiffusive regime is described within the free volume theory. Calculated values of self-diffusion coefficient are in agreement with quasielastic neutron scattering measurements. Self-diffusion coefficient is found to be composed of two factors: one is related to an area per lipid change at the phase transition, and the other one is due to an order of magnitude change in the stiffness of entropic repulsive potential.
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Affiliation(s)
- Boris Kheyfets
- National University of Science and Technology MISIS, Moscow, Russia
| | - Timur Galimzyanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Moscow, Russia
| | - Sergei Mukhin
- National University of Science and Technology MISIS, Moscow, Russia
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41
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Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH, Carlson LA, Bahrami AH, Goldman DH, Ren X, Hummer G, Bustamante C, Hurley JH. ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 2019; 362:1423-1428. [PMID: 30573630 DOI: 10.1126/science.aat1839] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/17/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022]
Abstract
The endosomal sorting complexes required for transport (ESCRTs) catalyze reverse-topology scission from the inner face of membrane necks in HIV budding, multivesicular endosome biogenesis, cytokinesis, and other pathways. We encapsulated ESCRT-III subunits Snf7, Vps24, and Vps2 and the AAA+ ATPase (adenosine triphosphatase) Vps4 in giant vesicles from which membrane nanotubes reflecting the correct topology of scission could be pulled. Upon ATP release by photo-uncaging, this system generated forces within the nanotubes that led to membrane scission in a manner dependent upon Vps4 catalytic activity and Vps4 coupling to the ESCRT-III proteins. Imaging of scission revealed Snf7 and Vps4 puncta within nanotubes whose presence followed ATP release, correlated with force generation and nanotube constriction, and preceded scission. These observations directly verify long-standing predictions that ATP-hydrolyzing assemblies of ESCRT-III and Vps4 sever membranes.
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Affiliation(s)
- Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Mark Remec Pavlin
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shannon Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maurizio Righini
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Il-Hyung Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lars-Anders Carlson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amir Houshang Bahrami
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Daniel H Goldman
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University, Frankfurt/M, Germany
| | - Carlos Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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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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43
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Kamerkar SC, Kraus F, Sharpe AJ, Pucadyil TJ, Ryan MT. Dynamin-related protein 1 has membrane constricting and severing abilities sufficient for mitochondrial and peroxisomal fission. Nat Commun 2018; 9:5239. [PMID: 30531964 PMCID: PMC6286342 DOI: 10.1038/s41467-018-07543-w] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Dynamin-related protein 1 (Drp1) is essential for mitochondrial and peroxisomal fission. Recent studies propose that Drp1 does not sever but rather constricts mitochondrial membranes allowing dynamin 2 (Dnm2) to execute final scission. Here, we report that unlike Drp1, Dnm2 is dispensable for peroxisomal and mitochondrial fission, as these events occurred in Dnm2 knockout cells. Fission events were also observed in mouse embryonic fibroblasts lacking Dnm1, 2 and 3. Using reconstitution experiments on preformed membrane tubes, we show that Drp1 alone both constricts and severs membrane tubes. Scission required the membrane binding, self-assembling and GTPase activities of Drp1 and occurred on tubes up to 250 nm in radius. In contrast, Dnm2 exhibited severely restricted fission capacity with occasional severing of tubes below 50 nm in radius. We conclude that Drp1 has both membrane constricting and severing abilities and is the dominant dynamin performing mitochondrial and peroxisomal fission. Drp1 and Dnm2 have been implicated in mitochondrial fission events, although their specific activities in constriction and scission have been unclear. Here, the authors demonstrate that Drp1 is sufficient to constrict and sever mitochondrial and peroxisomal membranes in the absence of Dnm proteins.
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Affiliation(s)
- Sukrut C Kamerkar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Felix Kraus
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia
| | - Thomas J Pucadyil
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800, Melbourne, Australia.
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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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45
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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46
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Bassereau P, Jin R, Baumgart T, Deserno M, Dimova R, Frolov VA, Bashkirov PV, Grubmüller H, Jahn R, Risselada HJ, Johannes L, Kozlov MM, Lipowsky R, Pucadyil TJ, Zeno WF, Stachowiak JC, Stamou D, Breuer A, Lauritsen L, Simon C, Sykes C, Voth GA, Weikl TR. The 2018 biomembrane curvature and remodeling roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:343001. [PMID: 30655651 PMCID: PMC6333427 DOI: 10.1088/1361-6463/aacb98] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds. On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo- and exocytosis, phagocytosis and filopodia formation. On the other hand, a multitude of intracellular processes at the level of organelles rely on generation, modulation, and maintenance of membrane curvature to maintain the organelle shape and functionality. The contribution of biophysicists and biologists is essential for shedding light on the mechanistic understanding and quantification of these processes. Given the vast complexity of phenomena and mechanisms involved in the coupling between membrane shape and function, it is not always clear in what direction to advance to eventually arrive at an exhaustive understanding of this important research area. The 2018 Biomembrane Curvature and Remodeling Roadmap of Journal of Physics D: Applied Physics addresses this need for clarity and is intended to provide guidance both for students who have just entered the field as well as established scientists who would like to improve their orientation within this fascinating area.
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Affiliation(s)
- Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Rui Jin
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Tobias Baumgart
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, United States of America
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - 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
| | - Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - H Jelger Risselada
- Department of Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Michael M Kozlov
- Sackler Faculty of Medicine, Department of Physiology and Pharmacology, Tel Aviv University
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | | | - Wade F Zeno
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Austin, TX, United States of America
| | - Dimitrios Stamou
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Artú Breuer
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Line Lauritsen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Camille Simon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Cécile Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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47
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Pucadyil TJ. A novel fluorescence microscopic approach to quantitatively analyse protein-induced membrane remodelling. J Biosci 2018. [DOI: 10.1007/s12038-018-9767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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48
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Pucadyil TJ. A novel fluorescence microscopic approach to quantitatively analyse protein-induced membrane remodelling. J Biosci 2018; 43:431-435. [PMID: 30002262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane remodelling or the bending and rupture of the lipid bilayer occurs during diverse cellular processes such as cell division, synaptic transmission, vesicular transport, organelle biogenesis and sporulation. These activities are brought about by the localized change in membrane curvature, which in turn causes lipid-packing stress, of a planar lipid bilayer by proteins. For instance, vesicular transport processes are typically characterized by the cooperative recruitment of proteins that induce budding of a planar membrane and catalyse fission of the necks of membrane buds to release vesicles. The analysis of such membrane remodelling reactions has traditionally been restricted to electron microscopy-based approaches or force spectroscopic analysis of membrane tethers pulled from liposome-based model membrane systems. Our recent work has demonstrated the facile creation of tubular model membrane systems of supported membrane tubes (SMrTs), which mimic late-stage intermediates of typical vesicular transport reactions. This review addresses the nature of such an assay system and a fluorescence-intensity-based analysis of changes in tube dimensions that is indicative of the membrane remodelling capacity of proteins.
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Affiliation(s)
- Thomas J Pucadyil
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, India,
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49
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Zhang G, Müller M. Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers. J Chem Phys 2018; 147:064906. [PMID: 28810752 DOI: 10.1063/1.4997575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale kBT.
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Affiliation(s)
- Guojie Zhang
- Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Marcus Müller
- Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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50
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Differential miRNA expression profiling reveals miR-205-3p to be a potential radiosensitizer for low- dose ionizing radiation in DLD-1 cells. Oncotarget 2018; 9:26387-26405. [PMID: 29899866 PMCID: PMC5995186 DOI: 10.18632/oncotarget.25405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/28/2018] [Indexed: 12/12/2022] Open
Abstract
Enhanced radiosensitivity at low doses of ionizing radiation (IR) (0.2 to 0.6 Gy) has been reported in several cell lines. This phenomenon, known as low doses hyper-radiosensitivity (LDHRS), appears as an opportunity to decrease toxicity of radiotherapy and to enhance the effects of chemotherapy. However, the effect of low single doses IR on cell death is subtle and the mechanism underlying LDHRS has not been clearly explained, limiting the utility of LDHRS for clinical applications. To understand the mechanisms responsible for cell death induced by low-dose IR, LDHRS was evaluated in DLD-1 human colorectal cancer cells and the expression of 80 microRNAs (miRNAs) was assessed by qPCR array. Our results show that DLD-1 cells display an early DNA damage response and apoptotic cell death when exposed to 0.6 Gy. miRNA expression profiling identified 3 over-expressed (miR-205-3p, miR-1 and miR-133b) and 2 down-regulated miRNAs (miR-122-5p, and miR-134-5p) upon exposure to 0.6 Gy. This miRNA profile differed from the one in cells exposed to high-dose IR (12 Gy), supporting a distinct low-dose radiation-induced cell death mechanism. Expression of a mimetic miR-205-3p, the most overexpressed miRNA in cells exposed to 0.6 Gy, induced apoptotic cell death and, more importantly, increased LDHRS in DLD-1 cells. Thus, we propose miR-205-3p as a potential radiosensitizer to low-dose IR.
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