1
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Lin SZ, Prost J, Rupprecht JF. Curvature-induced clustering of cell adhesion proteins. Phys Rev E 2024; 109:054406. [PMID: 38907394 DOI: 10.1103/physreve.109.054406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/02/2024] [Indexed: 06/24/2024]
Abstract
Cell adhesion proteins typically form stable clusters that anchor the cell membrane to its environment. Several works have suggested that cell membrane protein clusters can emerge from a local feedback between the membrane curvature and the density of proteins. Here, we investigate the effect of such a curvature-sensing mechanism in the context of cell adhesion proteins. We show how clustering emerges in an intermediate range of adhesion and curvature-sensing strengths. We identify key differences with the tilt-induced gradient sensing mechanism we previously proposed (Lin et al., arXiv:2307.03670).
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Affiliation(s)
- Shao-Zhen Lin
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living systems, Marseille, France
| | - Jacques Prost
- Laboratoire Physico-Chimie Curie, UMR 168, Institut Curie, PSL Research University, CNRS, Sorbonne Université, 75005 Paris, France
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Jean-François Rupprecht
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living systems, Marseille, France
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2
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Sadhu RK, Luciano M, Xi W, Martinez-Torres C, Schröder M, Blum C, Tarantola M, Villa S, Penič S, Iglič A, Beta C, Steinbock O, Bodenschatz E, Ladoux B, Gabriele S, Gov NS. A minimal physical model for curvotaxis driven by curved protein complexes at the cell's leading edge. Proc Natl Acad Sci U S A 2024; 121:e2306818121. [PMID: 38489386 PMCID: PMC10963004 DOI: 10.1073/pnas.2306818121] [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: 04/27/2023] [Accepted: 01/29/2024] [Indexed: 03/17/2024] Open
Abstract
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels, or highly curved protrusions of other cells. Recent in vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed "curvotaxis." The origin and underlying mechanism that gives rise to this curvature sensitivity are not well understood. Here, we employ a "minimal cell" model which is composed of a vesicle that contains curved membrane protein complexes, that exert protrusive forces on the membrane (representing the pressure due to actin polymerization). This minimal-cell model gives rise to spontaneous emergence of a motile phenotype, driven by a lamellipodia-like leading edge. By systematically screening the behavior of this model on different types of curved substrates (sinusoidal, cylinder, and tube), we show that minimal ingredients and energy terms capture the experimental data. The model recovers the observed migration on the sinusoidal substrate, where cells move along the grooves (minima), while avoiding motion along the ridges. In addition, the model predicts the tendency of cells to migrate circumferentially on convex substrates and axially on concave ones. Both of these predictions are verified experimentally, on several cell types. Altogether, our results identify the minimization of membrane-substrate adhesion energy and binding energy between the membrane protein complexes as key players of curvotaxis in cell migration.
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Affiliation(s)
- Raj Kumar Sadhu
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Marine Luciano
- Department of Biochemistry, University of Geneva, Geneva4 CH-1211, Switzerland
- Mechanobiology & Biomaterials Group, Research Institute for Biosciences, Center of Innovation and Research in Materials and Polymers, University of Mons, MonsB-7000, Belgium
| | - Wang Xi
- Universite Paris Cite, CNRS, Institut Jacques Monod, ParisF-75013, France
| | | | - Marcel Schröder
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Christoph Blum
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Marco Tarantola
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Stefano Villa
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Samo Penič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana1000, Slovenia
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana1000, Slovenia
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam14476, Germany
- Nano Life Science Institute, Kanazawa University, Kanazawa920-1192, Japan
| | - Oliver Steinbock
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL32306-4390
| | - Eberhard Bodenschatz
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Benoît Ladoux
- Universite Paris Cite, CNRS, Institut Jacques Monod, ParisF-75013, France
| | - Sylvain Gabriele
- Mechanobiology & Biomaterials Group, Research Institute for Biosciences, Center of Innovation and Research in Materials and Polymers, University of Mons, MonsB-7000, Belgium
| | - Nir S. Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot7610001, Israel
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3
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Farnudi A, Ejtehadi MR, Everaers R. Dynamics of fluid bilayer vesicles: Soft meshes and robust curvature energy discretization. Phys Rev E 2023; 108:015301. [PMID: 37583159 DOI: 10.1103/physreve.108.015301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/26/2023] [Indexed: 08/17/2023]
Abstract
Continuum models like the Helfrich Hamiltonian are widely used to describe fluid bilayer vesicles. Here we study the molecular dynamics compatible dynamics of the vertices of two-dimensional meshes representing the bilayer, whose in-plane motion is only weakly constrained. We show (i) that Jülicher's discretization of the curvature energy offers vastly superior robustness for soft meshes compared to the commonly employed expression by Gommper and Kroll and (ii) that for sufficiently soft meshes, the typical behavior of fluid bilayer vesicles can emerge even if the mesh connectivity remains fixed throughout the simulations. In particular, soft meshes can accommodate large shape transformations, and the model can generate the typical ℓ^{-4} signal for the amplitude of surface undulation modes of nearly spherical vesicles all the way up to the longest wavelength modes. Furthermore, we compare results for Newtonian, Langevin, and Brownian dynamics simulations of the mesh vertices to demonstrate that the internal friction of the membrane model is negligible, making it suitable for studying the internal dynamics of vesicles via coupling to hydrodynamic solvers or particle-based solvent models.
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Affiliation(s)
- Ali Farnudi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Ralf Everaers
- Ecole Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, F-69342 Lyon, France
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4
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Mesarec L, Góźdź W, Kralj-Iglič V, Kralj S, Iglič A. Coupling of nematic in-plane orientational ordering and equilibrium shapes of closed flexible nematic shells. Sci Rep 2023; 13:10663. [PMID: 37393271 DOI: 10.1038/s41598-023-37664-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023] Open
Abstract
The impact of the intrinsic curvature of in-plane orientationally ordered curved flexible nematic molecules attached to closed 3D flexible shells was studied numerically. A Helfrich-Landau-de Gennes-type mesoscopic approach was adopted where the flexible shell's curvature field and in-plane nematic field are coupled and concomitantly determined in the process of free energy minimisation. We demonstrate that this coupling has the potential to generate a rich diversity of qualitatively new shapes of closed 3D nematic shells and the corresponding specific in-plane orientational ordering textures, which strongly depend on the shell's volume-to-surface area ratio, so far not predicted in mesoscopic-type numerical studies of 3D shapes of closed flexible nematic shells.
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Affiliation(s)
- Luka Mesarec
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000, Ljubljana, Slovenia.
| | - Wojciech Góźdź
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Veronika Kralj-Iglič
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Zdravstvena 5, 1000, Ljubljana, Slovenia
| | - Samo Kralj
- Department of Physics, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška Cesta 160, 2000, Maribor, Slovenia
- Condensed Matter Physics Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška Cesta 25, 1000, Ljubljana, Slovenia
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5
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Jung M, Jung G, Schmid F. Stability of Branched Tubular Membrane Structures. PHYSICAL REVIEW LETTERS 2023; 130:148401. [PMID: 37084449 DOI: 10.1103/physrevlett.130.148401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/15/2023] [Indexed: 05/03/2023]
Abstract
We study the energetics and stability of branched tubular membrane structures by computer simulations of a triangulated network model. We find that triple (Y) junctions can be created and stabilized by applying mechanical forces, if the angle between branches is 120°. The same holds for tetrahedral junctions with tetraeder angles. If the wrong angles are enforced, the branches coalesce to a linear structure, a pure tube. After releasing the mechanical force, Y-branched structures remain metastable if one constrains the enclosed volume and the average curvature (the area difference) to a fixed value; tetrahedral junctions however split up into two Y junctions. Somewhat counterintuitively, the energy cost of adding a Y branch is negative in structures with fixed surface area and tube diameter, even if one accounts for the positive contribution of the additional branch end. For fixed average curvature, however, adding a branch also enforces a thinning of tubes, therefore the overall curvature energy cost is positive. Possible implications for the stability of branched networks structures in cells are discussed.
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Affiliation(s)
- Maike Jung
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Gerhard Jung
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, 34095 Montpellier, France
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
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6
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Pezeshkian W, Grünewald F, Narykov O, Lu S, Arkhipova V, Solodovnikov A, Wassenaar TA, Marrink SJ, Korkin D. Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure 2023; 31:492-503.e7. [PMID: 36870335 DOI: 10.1016/j.str.2023.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands
| | - Oleksandr Narykov
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Senbao Lu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, 9747AS Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands.
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA; Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA.
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7
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Saha T, Heuer A, Galic M. Systematic analysis of curvature-dependent lipid dynamics in a stochastic 3D membrane model. SOFT MATTER 2023; 19:1330-1341. [PMID: 36692259 DOI: 10.1039/d2sm01260j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
To minimize the free energy of the system, lipid membranes display curvature-dependent rearrangements at the local and global scale. The optimal membrane shape is generally approximated by averaging the curvature preference of individual lipids across the whole surface. Potential stress due to imperfections in lipid packing caused by local lipid inhomogeneities, however, is frequently neglected. Here, we developed a stochastic 3D membrane model to investigate the relevance of this parameter for shape-dependent lipid and membrane dynamics. A systematic analysis of the discretized Helfrich type Hamiltonian indicates that stress-energy arising from imperfections in packing is analogous to van der Waals interactions, jointly determining membrane shape and localization of curvature-sensitive lipids based on their relative strengths. Insights from this work can be used to characterize natural and design synthetic agents for membrane-shape changes.
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Affiliation(s)
- Tanumoy Saha
- Institute of Medical Physics and Biophysics, University of Muenster, Germany.
- Cells in Motion' Interfaculty Centre, University of Muenster, Germany.
- CIM-IMPRS Graduate School, Muenster, Germany
| | - Andreas Heuer
- Cells in Motion' Interfaculty Centre, University of Muenster, Germany.
- Institute of Physical Chemistry, University of Muenster, Germany
| | - Milos Galic
- Institute of Medical Physics and Biophysics, University of Muenster, Germany.
- Cells in Motion' Interfaculty Centre, University of Muenster, Germany.
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8
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Sadhu RK, Barger SR, Penič S, Iglič A, Krendel M, Gauthier NC, Gov NS. A theoretical model of efficient phagocytosis driven by curved membrane proteins and active cytoskeleton forces. SOFT MATTER 2022; 19:31-43. [PMID: 36472164 PMCID: PMC10078962 DOI: 10.1039/d2sm01152b] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phagocytosis is the process of engulfment and internalization of comparatively large particles by cells, and plays a central role in the functioning of our immune system. We study the process of phagocytosis by considering a simplified coarse grained model of a three-dimensional vesicle, having a uniform adhesion interaction with a rigid particle, and containing curved membrane-bound protein complexes or curved membrane nano-domains, which in turn recruit active cytoskeletal forces. Complete engulfment is achieved when the bending energy cost of the vesicle is balanced by the gain in the adhesion energy. The presence of curved (convex) proteins reduces the bending energy cost by self-organizing with a higher density at the highly curved leading edge of the engulfing membrane, which forms the circular rim of the phagocytic cup that wraps around the particle. This allows the engulfment to occur at much smaller adhesion strength. When the curved membrane-bound protein complexes locally recruit actin polymerization machinery, which leads to outward forces being exerted on the membrane, we found that engulfment is achieved more quickly and at a lower protein density. We consider spherical and non-spherical particles and found that non-spherical particles are more difficult to engulf in comparison to the spherical particles of the same surface area. For non-spherical particles, the engulfment time crucially depends on the initial orientation of the particles with respect to the vesicle. Our model offers a mechanism for the spontaneous self-organization of the actin cytoskeleton at the phagocytic cup, in good agreement with recent high-resolution experimental observations.
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Affiliation(s)
- Raj Kumar Sadhu
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Sarah R Barger
- Molecular, Cellular, Developmental Biology, Yale University, New Haven, USA
| | - Samo Penič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Mira Krendel
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, USA
| | | | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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9
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De Franceschi N, Pezeshkian W, Fragasso A, Bruininks BMH, Tsai S, Marrink SJ, Dekker C. Synthetic Membrane Shaper for Controlled Liposome Deformation. ACS NANO 2022; 17:966-978. [PMID: 36441529 PMCID: PMC9878720 DOI: 10.1021/acsnano.2c06125] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Shape defines the structure and function of cellular membranes. In cell division, the cell membrane deforms into a "dumbbell" shape, while organelles such as the autophagosome exhibit "stomatocyte" shapes. Bottom-up in vitro reconstitution of protein machineries that stabilize or resolve the membrane necks in such deformed liposome structures is of considerable interest to characterize their function. Here we develop a DNA-nanotechnology-based approach that we call the synthetic membrane shaper (SMS), where cholesterol-linked DNA structures attach to the liposome membrane to reproducibly generate high yields of stomatocytes and dumbbells. In silico simulations confirm the shape-stabilizing role of the SMS. We show that the SMS is fully compatible with protein reconstitution by assembling bacterial divisome proteins (DynaminA, FtsZ:ZipA) at the catenoidal neck of these membrane structures. The SMS approach provides a general tool for studying protein binding to complex membrane geometries that will greatly benefit synthetic cell research.
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Affiliation(s)
- Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Weria Pezeshkian
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
- The
Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, 17DK-2100Copenhagen, Denmark
| | - Alessio Fragasso
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Bart M. H. Bruininks
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Sean Tsai
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AGGroningen, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
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10
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Chelladurai R, Debnath K, Jana NR, Basu JK. Spontaneous formation and growth kinetics of lipid nanotubules induced by passive nanoparticles. SOFT MATTER 2022; 18:7082-7090. [PMID: 36043324 DOI: 10.1039/d2sm00900e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lipid nanotubules (LNTs) are conduits that form on the membranes of cells and organelles, and they are ubiquitous in all forms of life from archaea and bacteria to plants and mammals. The formation, shape and dynamics of these LNTs are critical for cellular functions, supporting the transport of myriad cellular cargoes as well as communication within and between cells, and they are also widely believed to be responsible for exploitation of host cells by pathogens for the spread of infection and diseases. In vitro kinetic control of LNT formation can considerably enhance the scope of utilization of these structures for disease control and therapy. Here we report a new paradigm for spontaneous lipid nanotubulation, capturing the dynamical regimes of growth, stabilization and retraction of the tubes through the binding of synthetic nanoparticles on supported lipid bilayers (SLBs). The tubulation is determined by the spontaneous binding-unbinding of nanoparticles on the LNTs. The presented methodology could be used to rectify malfunctioning cellular tubules or to prevent the pathogenic spread of diseases through inhibition of cell-to-cell nanotubule formation.
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Affiliation(s)
| | - Koushik Debnath
- Indian Association for the Cultivation of Science, Kolkata, India
| | - Nikhil R Jana
- Indian Association for the Cultivation of Science, Kolkata, India
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11
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Kumar G, Srivastava A. Membrane Remodeling Due to a Mixture of Multiple Types of Curvature Proteins. J Chem Theory Comput 2022; 18:5659-5671. [PMID: 35981766 DOI: 10.1021/acs.jctc.2c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family. We also study the effect of membrane anisotropy that manifests as differential binding affinity and organization of curvature proteins, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphology of deformed vesicles that depend on membrane tension, the curvatures and number of the participating proteins as well as on protein-protein and membrane-protein interactions.
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Affiliation(s)
- Gaurav Kumar
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
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12
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Noguchi H, Tozzi C, Arroyo M. Binding of anisotropic curvature-inducing proteins onto membrane tubes. SOFT MATTER 2022; 18:3384-3394. [PMID: 35416229 DOI: 10.1039/d2sm00274d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bin/Amphiphysin/Rvs superfamily proteins and other curvature-inducing proteins have anisotropic shapes and anisotropically bend biomembranes. Here, we report how the anisotropic proteins bind the membrane tube and are orientationally ordered using mean-field theory including an orientation-dependent excluded volume. The proteins exhibit a second-order or first-order nematic transition with increasing protein density depending on the radius of the membrane tube. The tube curvatures for the maximum protein binding and orientational order are different and varied by the protein density and rigidity. As the external force along the tube axis increases, a first-order transition from a large tube radius with low protein density to a small radius with high density occurs once, and subsequently, the protein orientation tilts to the tube-axis direction. When an isotropic bending energy is used for the proteins with an elliptic shape, the force-dependence curves become symmetric and the first-order transition occurs twice. This theory quantitatively reproduces the results of meshless membrane simulation for short proteins, whereas deviations are seen for long proteins owing to the formation of protein clusters.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
| | - Caterina Tozzi
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | - Marino Arroyo
- Universitat Politèdcnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain
- Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE), 08034 Barcelona, Spain
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13
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Vyas P, Kumar PBS, Das SL. Sorting of proteins with shape and curvature anisotropy on a lipid bilayer tube. SOFT MATTER 2022; 18:1653-1665. [PMID: 35132986 DOI: 10.1039/d2sm00077f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Curvature induced sorting of lipid membrane bound proteins has been widely studied through experiments that induce curvature variation in a giant unilamellar lipid-bilayer vesicle with adsorbed proteins by pulling thin cylindrical tethers. In the theoretical space, this has been supplemented with models that capture curvature dependent interaction between membrane and idealized protein particles, through free energy contributions. Many membrane proteins such as the BAR domain proteins are known to have extremely anisotropic shapes and soft interacting potentials, whereas the idealizations of protein particles explored in models have only assumed them as hard disk-like particles with curvature anisotropy. Here, we present a model of sorting of the proteins while including the effects of softness in their interaction potentials, shape anisotropy in the protein structure, and curvature anisotropy in the interactions with the membrane. This is based on a clean separation of free energy contributions from non-ideal fluid behavior of soft anisotropic particles and curvature interactions between proteins and membranes. We probe the behavior of the sorting function under limiting conditions and show that it converges to the previously derived models. In addition to this, we present a comparison of the variation in sorting ratio due to the observed variation in the shape parameter values in known membrane proteins. Finally, using published experimental data for membrane proteins, we perform fitting and derive model parameters. We observe that shape anisotropy adversely affects the sorting of proteins to a high curvature region, whereas curvature anisotropy and softer interaction between proteins favor sorting.
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Affiliation(s)
- Pranav Vyas
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 678623, India
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology Palakkad, Palakkad 678623, India
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14
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Dynamic mechanochemical feedback between curved membranes and BAR protein self-organization. Nat Commun 2021; 12:6550. [PMID: 34772909 PMCID: PMC8589976 DOI: 10.1038/s41467-021-26591-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
In many physiological situations, BAR proteins reshape membranes with pre-existing curvature (templates), contributing to essential cellular processes. However, the mechanism and the biological implications of this reshaping process remain unclear. Here we show, both experimentally and through modelling, that BAR proteins reshape low curvature membrane templates through a mechanochemical phase transition. This phenomenon depends on initial template shape and involves the co-existence and progressive transition between distinct local states in terms of molecular organization (protein arrangement and density) and membrane shape (template size and spherical versus cylindrical curvature). Further, we demonstrate in cells that this phenomenon enables a mechanotransduction mode, in which cellular stretch leads to the mechanical formation of membrane templates, which are then reshaped into tubules by BAR proteins. Our results demonstrate the interplay between membrane mechanics and BAR protein molecular organization, integrating curvature sensing and generation in a comprehensive framework with implications for cell mechanical responses.
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15
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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16
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Tozzi C, Walani N, Le Roux AL, Roca-Cusachs P, Arroyo M. A theory of ordering of elongated and curved proteins on membranes driven by density and curvature. SOFT MATTER 2021; 17:3367-3379. [PMID: 33644786 DOI: 10.1039/d0sm01733g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved and elongated, and hence may adopt different states of orientational order, from isotropic to maximize entropy to nematic as a result of crowding or to adapt to the curvature of the underlying membrane. Here, extending the classical work of Onsager for ordering in hard particle systems and that of [E. S. Nascimento et al., Phys. Rev. E, 2017, 96, 022704], we develop a mean-field density functional theory to predict the orientational order and evaluate the free energy of ensembles of elongated and curved objects on curved membranes. This theory depends on the microscopic properties of the particles and explains how a density-dependent isotropic-to-nematic transition is modified by anisotropic curvature. We also examine the coexistence of isotropic and nematic phases. This theory predicts how ordering depends on geometry but we assume here that the geometry is fixed. It also lays the ground to understand the interplay between membrane reshaping by BAR proteins and molecular order, examined by [Le Roux et al., submitted, 2020].
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Affiliation(s)
- Caterina Tozzi
- Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain.
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17
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Spangler EJ, Olinger AD, Kumar PBS, Laradji M. Binding, unbinding and aggregation of crescent-shaped nanoparticles on nanoscale tubular membranes. SOFT MATTER 2021; 17:1016-1027. [PMID: 33284936 DOI: 10.1039/d0sm01642j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Using molecular dynamics simulations of a coarse-grained implicit solvent model, we investigate the binding of crescent-shaped nanoparticles (NPs) on tubular lipid membranes. The NPs adhere to the membrane through their concave side. We found that the binding/unbinding transition is first-order, with the threshold binding energy being higher than the unbinding threshold, and the energy barrier between the bound and unbound states at the transition that increases with increasing the NP's arclength Lnp or curvature mismatch μ = Rc/Rnp, where Rc and Rnp are the radii of curvature of the tubular membrane and the NP, respectively. Furthermore, we found that the threshold binding energy increases with increasing either Lnp or μ. NPs with curvature larger than that of the tubule (μ > 1) lie perpendicularly to the tubule's axis. However, for μ smaller than a specific arclength-dependent mismatch μ*, the NPs are tilted with respect to the tubule's axis, with the tilt angle that increases with decreasing μ. We also investigated the self-assembly of the NPs on the tubule at relatively weak adhesion strength and found that for μ > 1 and high values of Lnp, the NPs self-assemble into linear chains, and lie side-by-side. For μ < μ* and high Lnp, the NPs also self-assemble into chains, while being tilted with respect to the tubule's axis.
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Affiliation(s)
- Eric J Spangler
- Department of Biomedical Engineering and Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA
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18
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Bonazzi F, Hall CK, Weikl TR. Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature. SOFT MATTER 2021; 17:268-275. [PMID: 32270169 DOI: 10.1039/c9sm02476j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological membranes are shaped by various proteins that either generate inward or outward membrane curvature. In this article, we investigate the membrane morphologies induced by mixtures of arc-shaped particles with coarse-grained modeling and simulations. The particles bind to the membranes either with their inward, concave side or their outward, convex side and, thus, generate membrane curvature of opposite sign. We find that small fractions of convex-binding particles can stabilize three-way junctions of membrane tubules, as suggested for the protein lunapark in the endoplasmic reticulum of cells. For comparable fractions of concave-binding and convex-binding particles, we observe lines of particles of the same type, and diverse membrane morphologies with grooves and bulges induced by these particle lines. The alignment and segregation of the particles is driven by indirect, membrane-mediated interactions.
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Affiliation(s)
- Francesco Bonazzi
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
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19
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Adhesion and Aggregation of Spherical Nanoparticles on Lipid Membranes. Chem Phys Lipids 2020; 233:104989. [PMID: 33120231 DOI: 10.1016/j.chemphyslip.2020.104989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 02/03/2023]
Abstract
We present a review of recent results on the adhesion, wrapping and aggregation of spherical nanoparticles (NPs) on lipid membranes via molecular dynamics simulations of an implicit solvent model. We show that the degree of wrapping of small NPs, by tensionless planar membranes, can increase continuously with the adhesion strength. However, the degree of wrapping exhibits a discontinuity for large NPs or short interaction range. The adhesion of NPs to small vesicles, without volume constraint, also exhibits a discontinuity between weakly wrapped states and fully endocytosed states. Multiple spherical NPs, bound to tensionless planar membranes are either in a gas state, at weak adhesion strength, or aggregate, at relatively high adhesion strength, into a multitude of structures, corresponding to in-plane chains, out-of-plane tubes and rings, and out-of-plane single-chain tubes. Annealing scans and free energy calculations show that the gas and tube phases are the predominantly stable phases. In-plane chains are only stable for small aggregates and the out-of-plane bitubes are long-lived metastable states.
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20
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Amphipathic molecules modulate PIEZO1 activity. Biochem Soc Trans 2020; 47:1833-1842. [PMID: 31754715 DOI: 10.1042/bst20190372] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/28/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023]
Abstract
PIEZO proteins are large eukaryotic mechanically-gated channels that function as homotrimers. The basic PIEZO1 structure has been elucidated by CryoEM and it assembles into a protein-lipid dome. A curved lipid region allows for the transition to the lipid bilayer from the dome (footprint). Gating PIEZO1 is mediated by bilayer tension that induces an area change in the lipid dome. The footprint region is thought to be energetically important for changes in lateral tension. Amphipathic molecules can modulate channel function beyond the intrinsic gating properties of PIEZO1. As a result, molecules that modify lipid properties within the lipid-channel complex (footprint and dome) will profoundly affect channel kinetics. In this review, we summarize the effects some amphipathic molecules have on the lipid bilayer and PIEZO1 function. PIEZO1 has three states, closed, open and inactivated and amphipathic molecules influence these transitions. The amphipathic peptide, GsMTx4, inhibits the closed to open transition. While saturated fatty acids also prevent PIEZO1 gating, the effect is mediated by stiffening the lipids, presumably in both the dome and footprint region. Polyunsaturated fatty acids can increase disorder within the lipid-protein complex affecting channel kinetics. PIEZO1 can also form higher-ordered structures that confers new kinetic properties associated with clustered channels. Cholesterol-rich domains house PIEZO1 channels, and depletion of cholesterol causes a breakdown of those domains with changes to channel kinetics and channel diffusion. These examples underscore the complex effects lipophilic molecules can have on the PIEZO1 lipid dome structure and thus on the mechanical response of the cell.
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21
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Pezeshkian W, Ipsen JH. Fluctuations and conformational stability of a membrane patch with curvature inducing inclusions. SOFT MATTER 2019; 15:9974-9981. [PMID: 31754667 DOI: 10.1039/c9sm01762c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membranes with curvature inducing inclusions display a range of cooperative phenomena, which can be linked to biomembrane function, e.g. membrane tubulation, vesiculation, softening and spontaneous tension. We investigate how these phenomena are related for a fluctuating, framed membrane through analysis of a descretized membrane model by Monte Carlo simulation techniques. The membrane model is based on a dynamically triangulated surface equipped with non-interacting, up-down symmetry breaking inclusions where only terms coupled linearly to mean-curvature are maintained. We show that the lateral configurational entropy plays a key role for the mechanical properties of the semi-flexible membrane, e.g. a pronounced softening at intermediate inclusion coverages of the membrane and generation of membrane tension. Tensionless framed membranes will remain quasi-flat up to some threshold coverage, where a shape instability occurs with formation of pearling or tubular membranes, which below full coverage is associated with segregation of inclusions between the curved and flat membrane geometries. For inclusions with preference for highly curved membranes the instability appears at dilute inclusion coverages and is accompanied by strong configurational fluctuations.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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22
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Simunovic M, Evergren E, Callan-Jones A, Bassereau P. Curving Cells Inside and Out: Roles of BAR Domain Proteins in Membrane Shaping and Its Cellular Implications. Annu Rev Cell Dev Biol 2019; 35:111-129. [DOI: 10.1146/annurev-cellbio-100617-060558] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many cellular processes rely on precise and timely deformation of the cell membrane. While many proteins participate in membrane reshaping and scission, usually in highly specialized ways, Bin/amphiphysin/Rvs (BAR) domain proteins play a pervasive role, as they not only participate in many aspects of cell trafficking but also are highly versatile membrane remodelers. Subtle changes in the shape and size of the BAR domain can greatly impact the way in which BAR domain proteins interact with the membrane. Furthermore, the activity of BAR domain proteins can be tuned by external physical parameters, and so they behave differently depending on protein surface density, membrane tension, or membrane shape. These proteins can form 3D structures that mold the membrane and alter its liquid properties, even promoting scission under various circumstances.As such, BAR domain proteins have numerous roles within the cell. Endocytosis is among the most highly studied processes in which BAR domain proteins take on important roles. Over the years, a more complete picture has emerged in which BAR domain proteins are tied to almost all intracellular compartments; examples include endosomal sorting and tubular networks in the endoplasmic reticulum and T-tubules. These proteins also have a role in autophagy, and their activity has been linked with cancer. Here, we briefly review the history of BAR domain protein discovery, discuss the mechanisms by which BAR domain proteins induce curvature, and attempt to settle important controversies in the field. Finally, we review BAR domain proteins in the context of a cell, highlighting their emerging roles in cell signaling and organelle shaping.
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Affiliation(s)
- Mijo Simunovic
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Emma Evergren
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Andrew Callan-Jones
- Laboratoire Matière et Systèmes Complexes, CNRS UMR 7057, 75205 Paris, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
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23
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Pezeshkian W, König M, Marrink SJ, Ipsen JH. A Multi-Scale Approach to Membrane Remodeling Processes. Front Mol Biosci 2019; 6:59. [PMID: 31396522 PMCID: PMC6664084 DOI: 10.3389/fmolb.2019.00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - John H Ipsen
- Department of Physics, Chemistry and Pharmacy, Center for Biomembrane Physics (MEMPHYS), University of Southern Denmark, Odense, Denmark
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24
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Jarin Z, Tsai FC, Davtyan A, Pak AJ, Bassereau P, Voth GA. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys J 2019; 117:553-562. [PMID: 31349990 PMCID: PMC6697384 DOI: 10.1016/j.bpj.2019.06.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated membrane remodeling is a ubiquitous and critical process for proper cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane deformation as a precursor to large-scale membrane remodeling. We employ a multiscale approach to provide the molecular mechanism of unusual I-BAR domain-driven membrane remodeling at a low protein surface concentration with near-atomistic detail. We generate a bottom-up coarse-grained model that demonstrates similar membrane-bound I-BAR domain aggregation behavior as our recent Mesoscopic Membrane with Explicit Proteins model. Together, these models bridge several length scales and reveal an aggregation behavior of I-BAR domains. We find that at low surface coverage (i.e., low bound protein density), I-BAR domains form transient, tip-to-tip strings on periodic flat membrane sheets. Inside of lipid bilayer tubules, we find linear aggregates parallel to the axis of the tubule. Finally, we find that I-BAR domains form tip-to-tip aggregates around the edges of membrane domes. These results are supported by in vitro experiments showing low curvature bulges surrounded by I-BAR domains on giant unilamellar vesicles. Overall, our models reveal new I-BAR domain aggregation behavior in membrane tubules and on the surface of vesicles at low surface concentration that add insight into how I-BAR domain proteins may contribute to certain aspects of membrane remodeling in cells.
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Affiliation(s)
- Zack Jarin
- Pritzker School for Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Feng-Ching Tsai
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Aram Davtyan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Alexander J Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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25
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Idema T, Kraft DJ. Interactions between model inclusions on closed lipid bilayer membranes. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Bonazzi F, Weikl TR. Membrane Morphologies Induced by Arc-Shaped Scaffolds Are Determined by Arc Angle and Coverage. Biophys J 2019; 116:1239-1247. [PMID: 30902368 DOI: 10.1016/j.bpj.2019.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 01/13/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022] Open
Abstract
The intricate shapes of biological membranes such as tubules and membrane stacks are induced by proteins. In this article, we systematically investigate the membrane shapes induced by arc-shaped scaffolds such as proteins and protein complexes with coarse-grained modeling and simulations. We find that arc-shaped scaffolds induce membrane tubules at membrane coverages larger than a threshold of ∼40%, irrespective of their arc angle. The membrane morphologies at intermediate coverages below this tubulation threshold, in contrast, strongly depend on the arc angle. Scaffolds with arc angles of about 60°, akin to N-BAR domains, do not change the membrane shape at coverages below the tubulation threshold, whereas scaffolds with arc angles larger than about 120° induce double-membrane stacks at intermediate coverages. The scaffolds stabilize the curved membrane edges that connect the membrane stacks, as suggested for complexes of reticulon proteins. Our results provide general insights on the determinants of membrane shaping by arc-shaped scaffolds.
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Affiliation(s)
- Francesco Bonazzi
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Potsdam, Germany.
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27
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Kumar G, Ramakrishnan N, Sain A. Tubulation pattern of membrane vesicles coated with biofilaments. Phys Rev E 2019; 99:022414. [PMID: 30934309 DOI: 10.1103/physreve.99.022414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Indexed: 06/09/2023]
Abstract
Narrow membrane tubes are commonly pulled out from the surface of phospholipid vesicles using forces applied either through laser or magnetic tweezers or through the action of processive motor proteins. Recent examples have emerged in which an array of such tubes grows spontaneously from vesicles coated with bioactive cytoskeletal filaments (e.g., FtsZ, microtubule) in the presence GTP or ATP. We show how a soft vesicle deforms as a result of the interplay between its topology, local curvature, and the forces due to filament bundles. We present results from dynamically triangulated Monte Carlo simulations of a closed membrane vesicle coated with a nematic field (the filaments), and we show how the intrinsic curvature of the filaments and their bundling interactions drive membrane tubulation. We predict interesting patterns consisting of a large number of nematic defects that accompany tubulation. A common theme emerges: defect locations on vesicle surfaces are hot spots of membrane deformation activity, which could be useful for vesicle origami. Although our equilibrium model is not applicable to the nonequilibrium shape dynamics exhibited by active microtubule-coated vesicles, we show that some of the features, such as the size-dependent vesicle shape and the number of tubes, can still be understood from our equilibrium model.
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Affiliation(s)
- Gaurav Kumar
- Physics Department, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
| | - N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Anirban Sain
- Physics Department, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, India
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28
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Jamin N, Garrigos M, Jaxel C, Frelet-Barrand A, Orlowski S. Ectopic Neo-Formed Intracellular Membranes in Escherichia coli: A Response to Membrane Protein-Induced Stress Involving Membrane Curvature and Domains. Biomolecules 2018; 8:biom8030088. [PMID: 30181516 PMCID: PMC6163855 DOI: 10.3390/biom8030088] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/31/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
Bacterial cytoplasmic membrane stress induced by the overexpression of membrane proteins at high levels can lead to formation of ectopic intracellular membranes. In this review, we report the various observations of such membranes in Escherichia coli, compare their morphological and biochemical characterizations, and we analyze the underlying molecular processes leading to their formation. Actually, these membranes display either vesicular or tubular structures, are separated or connected to the cytoplasmic membrane, present mono- or polydispersed sizes and shapes, and possess ordered or disordered arrangements. Moreover, their composition differs from that of the cytoplasmic membrane, with high amounts of the overexpressed membrane protein and altered lipid-to-protein ratio and cardiolipin content. These data reveal the importance of membrane domains, based on local specific lipid⁻protein and protein⁻protein interactions, with both being crucial for local membrane curvature generation, and they highlight the strong influence of protein structure. Indeed, whether the cylindrically or spherically curvature-active proteins are actively curvogenic or passively curvophilic, the underlying molecular scenarios are different and can be correlated with the morphological features of the neo-formed internal membranes. Delineating these molecular mechanisms is highly desirable for a better understanding of protein⁻lipid interactions within membrane domains, and for optimization of high-level membrane protein production in E. coli.
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Affiliation(s)
- Nadège Jamin
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Manuel Garrigos
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Christine Jaxel
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Annie Frelet-Barrand
- Institut FEMTO-ST, UMR CNRS 6174, Université Bourgogne Franche-Comté, 15B avenue des Montboucons, 25030 Besançon CEDEX, France.
| | - Stéphane Orlowski
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
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29
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Simunovic M, Bassereau P, Voth GA. Organizing membrane-curving proteins: the emerging dynamical picture. Curr Opin Struct Biol 2018; 51:99-105. [PMID: 29609179 PMCID: PMC6165709 DOI: 10.1016/j.sbi.2018.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 11/30/2022]
Abstract
Lipid membranes play key roles in cells, such as in trafficking, division, infection, remodeling of organelles, among others. The key step in all these processes is creating membrane curvature, typically under the control of many anchored, adhered or included proteins. However, it has become clear that the membrane itself can mediate the interactions among proteins to produce highly ordered assemblies. Computer simulations are ideally suited to investigate protein organization and the dynamics of membrane remodeling at near-micron scales, something that is extremely challenging to tackle experimentally. We review recent computational efforts in modeling protein-caused membrane deformation mechanisms, specifically focusing on coarse-grained simulations. We highlight work that exposed the membrane-mediated ordering of proteins into lines, meshwork, spirals and other assemblies, in what seems to be a very generic mechanism driven by a combination of short and long-ranged forces. Modulating the mechanical properties of membranes is an underexplored signaling mechanism in various processes deserving of more attention in the near future.
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Affiliation(s)
- Mijo Simunovic
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, Chicago, IL 60637, USA; Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France; Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, Chicago, IL 60637, USA.
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30
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Ramakrishnan N, Bradley RP, Tourdot RW, Radhakrishnan R. Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:273001. [PMID: 29786613 PMCID: PMC6066392 DOI: 10.1088/1361-648x/aac702] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.
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Affiliation(s)
- N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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31
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Spangler EJ, Kumar PBS, Laradji M. Stability of membrane-induced self-assemblies of spherical nanoparticles. SOFT MATTER 2018; 14:5019-5030. [PMID: 29855646 DOI: 10.1039/c8sm00537k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The self-assembly of spherical nanoparticles, resulting from their adhesion on tensionless lipid membranes, is investigated through molecular dynamics simulations of a coarse-grained implicit-solvent model. Our simulations indicate that, with increasing adhesion strength, while reshaping the membrane, the nanoparticles aggregate into a sequence of self-assemblies corresponding to in-plane chains, two-row tubular (bitube) chains, annular (ring) chains, and single-row tubular (tube) chains. Annealing scans, with respect to adhesion strength, show that the transitions between the various phases are highly first-order with significant hystereses. Free energy calculations indicate that the gas and single-row tubular chains are stable over wide ranges of adhesion strength. In contrast, the in-plane chains are only stable for small aggregates of NPs, and the bitube and ring chains are long-lived metastable states over a wide range of adhesion strength.
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Affiliation(s)
- Eric J Spangler
- Department of Biomedical Engineering, The University of Memphis, Memphis, TN 38152, USA
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32
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Sreeja KK, Sunil Kumar PB. Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles. J Chem Phys 2018; 148:134703. [PMID: 29626906 DOI: 10.1063/1.5022494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten their aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations, the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.
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Affiliation(s)
- K K Sreeja
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
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33
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Johannes L, Pezeshkian W, Ipsen JH, Shillcock JC. Clustering on Membranes: Fluctuations and More. Trends Cell Biol 2018; 28:405-415. [PMID: 29502867 DOI: 10.1016/j.tcb.2018.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/18/2022]
Abstract
Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions.
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Affiliation(s)
- Ludger Johannes
- Institut Curie, PSL Research University, Cellular and Chemical Biology unit, INSERM U 1143, CNRS UMR 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
| | - Weria Pezeshkian
- Center for Biomembrane Physics (MEMPHYS), Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - John H Ipsen
- Center for Biomembrane Physics (MEMPHYS), Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Julian C Shillcock
- Blue Brain Project, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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34
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Elías-Wolff F, Lindén M, Lyubartsev AP, Brandt EG. Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling. J Chem Theory Comput 2018; 14:1643-1655. [PMID: 29350922 DOI: 10.1021/acs.jctc.7b00878] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch. This buckling approach samples a wide range of curvatures in a single simulation, and anisotropic effects can be extracted from the orientation statistics. We develop an efficient and robust algorithm to extract the motion of the probe along the buckled membrane surface, and evaluate its numerical properties by extensive sampling of three coarse-grained model systems: local lipid density in a curved environment for single-component bilayers, curvature preferences of individual lipids in two-component membranes, and curvature sensing by a homotrimeric transmembrane protein. The method can be used to complement experimental data from curvature partition assays and provides additional insight into mesoscopic theories and molecular mechanisms for curvature sensing.
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Affiliation(s)
- Federico Elías-Wolff
- Department of Biochemistry and Biophysics , Stockholm University , SE-106 91 Stockholm , Sweden.,Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Martin Lindén
- Department of Cell and Molecular Biology , Uppsala University , SE-751 05 Uppsala , Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Erik G Brandt
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 Stockholm , Sweden
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35
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Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-Range Organization of Membrane-Curving Proteins. ACS CENTRAL SCIENCE 2017; 3:1246-1253. [PMID: 29296664 PMCID: PMC5746856 DOI: 10.1021/acscentsci.7b00392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 05/02/2023]
Abstract
Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell.
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Affiliation(s)
- Mijo Simunovic
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Anđela Šarić
- Department
of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - J. Michael Henderson
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ka Yee C. Lee
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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36
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Noguchi H. Acceleration and suppression of banana-shaped-protein-induced tubulation by addition of small membrane inclusions of isotropic spontaneous curvatures. SOFT MATTER 2017; 13:7771-7779. [PMID: 29018843 DOI: 10.1039/c7sm01375b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Membrane tubulation induced by banana-shaped protein rods is investigated by using coarse-grained meshless membrane simulations. It is found that tubulation is promoted by laterally isotropic membrane inclusions that generate the same sign of spontaneous curvature as the adsorbed protein rods. The inclusions are concentrated in the tubules and reduce the bending energy of the tip of the tubules. On the other hand, inclusions with an opposite curvature suppress tubulation by percolated-network formation at a high protein-rod density while they induce the formation of a spherical membrane bud at a low rod density. When equal amounts of the two types of inclusions (with positive and negative curvatures) are added, their effects cancel each other for the first short period but later the tubulation is slowly accelerated. Positive surface tension suppresses tubulation. Our results suggest that the cooperation of scaffolding of BAR (Bin/Amphiphysin/Rvs) domains and isotropic membrane inclusions is important for tubulation.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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37
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Petrova AB, Herold C, Petrov EP. Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes. SOFT MATTER 2017; 13:7172-7187. [PMID: 28930355 DOI: 10.1039/c7sm00829e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 μm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.
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Affiliation(s)
- Anastasiia B Petrova
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, 82152 Martinsried, Germany.
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38
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Chabanon M, Stachowiak JC, Rangamani P. Systems biology of cellular membranes: a convergence with biophysics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2017; 9:10.1002/wsbm.1386. [PMID: 28475297 PMCID: PMC5561455 DOI: 10.1002/wsbm.1386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 12/12/2022]
Abstract
Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Morgan Chabanon
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
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39
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Davtyan A, Simunovic M, Voth GA. The mesoscopic membrane with proteins (MesM-P) model. J Chem Phys 2017; 147:044101. [PMID: 28764362 PMCID: PMC5552407 DOI: 10.1063/1.4993514] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 12/30/2022] Open
Abstract
We present the Mesoscopic Membrane with Proteins (MesM-P) model, an extension of a previously developed elastic membrane model for mesoscale simulations of lipid membranes. MesM-P employs a discrete mesoscopic quasi-particle approach to model protein-facilitated shape and topology changes of the lipid membrane on length and time scales inaccessible to all-atom and quasimolecular coarse-grained molecular dynamics simulations. We investigate the ability of MesM-P to model the behavior of large lipid vesicles as a function of bound protein density. We find four distinct mechanisms for protein aggregation on the surface of the membrane, depending on membrane stiffness and protein spontaneous curvature. We also establish a connection between MesM-P and the results of higher resolution coarse-grained molecular dynamics simulations.
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Affiliation(s)
- Aram Davtyan
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Mijo Simunovic
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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40
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Noguchi H. Construction of Nuclear Envelope Shape by a High-Genus Vesicle with Pore-Size Constraint. Biophys J 2017; 111:824-831. [PMID: 27558725 DOI: 10.1016/j.bpj.2016.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/15/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023] Open
Abstract
Nuclear pores have an approximately uniform distribution in the nuclear envelope of most living cells. Hence, the morphology of the nuclear envelope is a spherical stomatocyte with a high genus. We have investigated the morphology of high-genus vesicles under pore-size constraint using dynamically triangulated membrane simulations. Bending-energy minimization without volume or other constraints produces a circular-cage stomatocyte, where the pores are aligned in a circular line on an oblate bud. As the pore radius is reduced, the circular-pore alignment is more stabilized than a random pore distribution on a spherical bud. However, we have clarified the conditions for the formation of a spherical stomatocyte: a small perinuclear volume, osmotic pressure within nucleoplasm, and repulsion between the pores. When area-difference elasticity is taken into account, the formation of cylindrical or budded tubules from the stomatocyte and discoidal stomatocyte is found.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, Japan.
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41
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Noguchi H, Fournier JB. Membrane structure formation induced by two types of banana-shaped proteins. SOFT MATTER 2017; 13:4099-4111. [PMID: 28540958 DOI: 10.1039/c7sm00305f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The assembly of banana-shaped rodlike proteins on membranes and the associated membrane shape transformations are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two banana-shaped inclusions are derived theoretically using a point-like formalism based on fixed anisotropic curvatures, both for zero surface tension and for finite surface tension. On a larger scale, the interactions between the assemblies of such rodlike inclusions are determined analytically. Meshless membrane simulations are performed in the presence of a large number of inclusions of two types, corresponding to the curved rods of opposite curvatures, both for flat membranes and vesicles. Rods of the same type aggregate into linear assemblies perpendicular to the rod axis, leading to membrane tubulation. However, rods of the other type, those of opposite curvature, are attracted to the lateral sides of these assemblies, and stabilize a straight bump structure that prevents tubulation. When the two types of rods have almost opposite curvatures, the bumps attract one another, forming a striped structure. Positive surface tension is found to stabilize stripe formation. The simulation results agree well with the theoretical predictions provided the point-like curvatures of the model are scaled-down to account for the effective flexibility of the simulated rods.
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Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
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42
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Duan X, Yao Z. Curvature-driven stability of defects in nematic textures over spherical disks. Phys Rev E 2017; 95:062706. [PMID: 28709326 DOI: 10.1103/physreve.95.062706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Stabilizing defects in liquid-crystal systems is crucial for many physical processes and applications ranging from functionalizing liquid-crystal textures to recently reported command of chaotic behaviors of active matters. In this work, we perform analytical calculations to study the curvature-driven stability mechanism of defects based on the isotropic nematic disk model that is free of any topological constraint. We show that in a growing spherical disk covering a sphere the accumulation of curvature effect can prevent typical +1 and +1/2 defects from forming boojum textures where the defects are repelled to the boundary of the disk. Our calculations reveal that the movement of the equilibrium position of the +1 defect from the boundary to the center of the spherical disk occurs in a very narrow window of the disk area, exhibiting the first-order phase-transition-like behavior. For the pair of +1/2 defects by splitting a +1 defect, we find the curvature-driven alternating repulsive and attractive interactions between the two defects. With the growth of the spherical disk these two defects tend to approach and finally recombine towards a +1 defect texture. The sensitive response of defects to curvature and the curvature-driven stability mechanism demonstrated in this work in nematic disk systems may have implications towards versatile control and engineering of liquid-crystal textures in various applications.
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Affiliation(s)
- Xiuqing Duan
- School of Physics and Astronomy, and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenwei Yao
- School of Physics and Astronomy, and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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43
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Okuda S, Eiraku M. Role of molecular turnover in dynamic deformation of a three-dimensional cellular membrane. Biomech Model Mechanobiol 2017; 16:1805-1818. [PMID: 28555369 PMCID: PMC5599494 DOI: 10.1007/s10237-017-0920-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/13/2017] [Indexed: 11/26/2022]
Abstract
In cells, the molecular constituents of membranes are dynamically turned over by transportation from one membrane to another. This molecular turnover causes the membrane to shrink or expand by sensing the stress state within the cell, changing its morphology. At present, little is known as to how this turnover regulates the dynamic deformation of cellular membranes. In this study, we propose a new physical model by which molecular turnover is coupled with three-dimensional membrane deformation to explore mechanosensing roles of turnover in cellular membrane deformations. In particular, as an example of microscopic machinery, based on a coarse-graining description, we suppose that molecular turnover depends on the local membrane strain. Using the proposed model, we demonstrate computational simulations of a single vesicle. The results show that molecular turnover adaptively facilitates vesicle deformation, owing to its stress dependence; while the vesicle drastically expands in the case with low bending rigidity, it shrinks in that with high bending rigidity. Moreover, localized active tension on the membrane causes cellular migration by driving the directional transport of molecules within the cell. These results illustrate the use of the proposed model as well as the role of turnover in the dynamic deformations of cellular membranes.
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Affiliation(s)
- Satoru Okuda
- Laboratory for in vitro Histogenesis, Center for Developmental Biology (CDB), RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Mototsugu Eiraku
- Laboratory for in vitro Histogenesis, Center for Developmental Biology (CDB), RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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44
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Tachikawa M, Mochizuki A. Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics. Proc Natl Acad Sci U S A 2017; 114:5177-5182. [PMID: 28461510 PMCID: PMC5441826 DOI: 10.1073/pnas.1619264114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Golgi apparatus is a membrane-bounded organelle with the characteristic shape of a series of stacked flat cisternae. During mitosis in mammalian cells, the Golgi apparatus is once fragmented into small vesicles and then reassembled to form the characteristic shape again in each daughter cell. The mechanism and details of the reassembly process remain elusive. Here, by the physical simulation of a coarse-grained membrane model, we reconstructed the three-dimensional morphological dynamics of the Golgi reassembly process. Considering the stability of the interphase Golgi shape, we introduce two hypothetical mechanisms-the Golgi rim stabilizer protein and curvature-dependent restriction on membrane fusion-into the general biomembrane model. We show that the characteristic Golgi shape is spontaneously organized from the assembly of vesicles by proper tuning of the two additional mechanisms, i.e., the Golgi reassembly process is modeled as self-organization. We also demonstrate that the fine Golgi shape forms via a balance of three reaction speeds: vesicle aggregation, membrane fusion, and shape relaxation. Moreover, the membrane fusion activity decreases thickness and the number of stacked cisternae of the emerging shapes.
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Affiliation(s)
- Masashi Tachikawa
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan;
- Interdisciplinary Theoretical Science Research Group, RIKEN, Wako 351-0198, Japan
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
- Interdisciplinary Theoretical Science Research Group, RIKEN, Wako 351-0198, Japan
- Core Research for Evolutionary Science and Technology, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
- Interdisciplinary Theoretical and Mathematical Science Program, RIKEN, Wako 351-0198, Japan
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45
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Mesarec L, Góźdź W, Kralj S, Fošnarič M, Penič S, Kralj-Iglič V, Iglič A. On the role of external force of actin filaments in the formation of tubular protrusions of closed membrane shapes with anisotropic membrane components. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:705-718. [PMID: 28488019 DOI: 10.1007/s00249-017-1212-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 02/08/2023]
Abstract
Biological membranes are composed of different components and there is no a priori reason to assume that all components are isotropic. It was previously shown that the anisotropic properties of membrane components may explain the stability of membrane tubular protrusions even without the application of external force. Our theoretical study focuses on the role of anisotropic membrane components in the stability of membrane tubular structures generated or stabilized by actin filaments. We show that the growth of the actin cytoskeleton inside the vesicle can induce the partial lateral segregation of different membrane components. The entropy of mixing of membrane components hinders the total lateral segregation of the anisotropic and isotropic membrane components. Self-assembled aggregates formed by anisotropic membrane components facilitate the growth of long membrane tubular protrusions. Protrusive force generated by actin filaments favors strong segregation of membrane components by diminishing the opposing effect of mixing entropy.
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Affiliation(s)
- Luka Mesarec
- Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, 1000, Ljubljana, Slovenia.
| | - Wojciech Góźdź
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Samo Kralj
- Department of Physics, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia.,Jožef Stefan Institute, PO Box 3000, 1000, Ljubljana, Slovenia
| | - Miha Fošnarič
- Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, 1000, Ljubljana, Slovenia
| | - Samo Penič
- Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, 1000, Ljubljana, Slovenia
| | - Veronika Kralj-Iglič
- Laboratory of Clinical Biophysics, Faculty of Health Sciences, University of Ljubljana, Zdravstvena 5, 1000, Ljubljana, Slovenia.,Laboratory of Clinical Biophysics, Faculty of Medicine, University of Ljubljana, Zaloška 9, 1000, Ljubljana, Slovenia
| | - Aleš Iglič
- Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, 1000, Ljubljana, Slovenia.,Laboratory of Clinical Biophysics, Faculty of Medicine, University of Ljubljana, Zaloška 9, 1000, Ljubljana, Slovenia
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46
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Golushko IY, Rochal SB, Lorman VL. Multipole analysis of the strain-mediated coupling between proteins adsorbed at tubular lipid membrane surface. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:128. [PMID: 28000047 DOI: 10.1140/epje/i2016-16128-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
The tubular lipid membranes (TLMs) pulled out from vesicles are often used in in vitro studies of the interactions between curvature-inducing proteins and highly curved membranes. The protein molecules adsorbed at the membrane surface deform the TLM and couple with each other due to the induced strain. Here we propose an approach which models the single curvature-inducing protein action on the lipid bilayer by the multipole, the superposition of the point forces applied to the membrane in the region of the protein adsorption. We show that to be localized in the area of the protein size at the TLM surface, the force multipoles satisfying the mechanical equilibrium conditions should be composed of three or more point forces. The protein coupling energy mediated by the membrane strain is studied in detail. In the region of the tubular membrane stability the maximal distance between two neighboring interacting protein-induced force multipoles is estimated to be of the order of the TLM cross section perimeter. In the vicinity of the TLM instability in the region of the vanishing stretching force applied to the TLM, the interaction radius increases drastically. The high affinity of the single curvature-inducing protein molecule to the regions in the vicinity of the TLM ends is explained and related to the boundary conditions in the experimental set-ups. The reasons for the aggregate formation on the membrane surface are also discussed.
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Affiliation(s)
- I Yu Golushko
- Faculty of Physics, Southern Federal University, 5 Zorge Street, 344090, Rostov-on-Don, Russia.
| | - S B Rochal
- Faculty of Physics, Southern Federal University, 5 Zorge Street, 344090, Rostov-on-Don, Russia
| | - V L Lorman
- Laboratoire Charles Coulomb, UMR 5221 CNRS - Université de Montpellier, Place E. Bataillon, F-34095, Montpellier Cedex 5, France
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Agrawal H, Liu L, Sharma P. Revisiting the curvature-mediated interactions between proteins in biological membranes. SOFT MATTER 2016; 12:8907-8918. [PMID: 27725970 DOI: 10.1039/c6sm01572g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins embedded in soft biological membranes experience a long-range force mediated by elastic curvature deformations. The classical linearized Helfrich-Canham Hamiltonian based derivations reveal the nature of the force between a pair of proteins to be repulsive in the zero-temperature limit and the interaction potential is inversely proportional to the fourth power of the distance separating the inclusions. Such a result is the starting point to understand many-body interactions between proteins in biological membranes and the study of their clustering or, more broadly, self-organization. A key observation regarding this widely quoted result is that any two (mechanically rigid) proteins will experience an identical force. In other words, there is no specificity in the currently employed continuum models that purport to explain protein interactions. In this work we argue that each protein has a unique mechanical signature based on its interaction with the surrounding lipid bilayer membrane and cannot be treated as a non-specific rigid object. We modify the classical Helfrich-Canham theory of curvature elasticity to incorporate protein-membrane specificity, discuss the estimation of the new model parameters via atomistic simulations and re-evaluate the curvature-mediated force between proteins. We find that the incorporation of protein-specificity can reduce the interaction force by several orders of magnitude. Our result may provide at least one plausible reason behind why in some computational and experimental studies, a net attractive force between proteins is in evidence.
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Affiliation(s)
- Himani Agrawal
- Department of Mechanical Engineering, University of Houston, TX, USA
| | - Liping Liu
- Department of Mathematics and Department of Mechanical Aerospace Engineering, Rutgers University, NJ, USA.
| | - Pradeep Sharma
- Department of Mechanical Engineering and Department of Physics, University of Houston, TX, USA.
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48
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Gómez-Llobregat J, Elías-Wolff F, Lindén M. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides. Biophys J 2016; 110:197-204. [PMID: 26745422 DOI: 10.1016/j.bpj.2015.11.3512] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/29/2015] [Accepted: 11/11/2015] [Indexed: 12/29/2022] Open
Abstract
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins.
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Affiliation(s)
- Jordi Gómez-Llobregat
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Federico Elías-Wolff
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Martin Lindén
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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How curvature-generating proteins build scaffolds on membrane nanotubes. Proc Natl Acad Sci U S A 2016; 113:11226-11231. [PMID: 27655892 DOI: 10.1073/pnas.1606943113] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex subcellular structures, and many other cellular phenomena. They form 3D assemblies that act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we use various experimental, theoretical, and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube's length. Our work implies that the nature of local protein-membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30-40% of a tube's surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes.
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50
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Simunovic M, Prévost C, Callan-Jones A, Bassereau P. Physical basis of some membrane shaping mechanisms. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0034. [PMID: 27298443 PMCID: PMC4920286 DOI: 10.1098/rsta.2016.0034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 05/24/2023]
Abstract
In vesicular transport pathways, membrane proteins and lipids are internalized, externalized or transported within cells, not by bulk diffusion of single molecules, but embedded in the membrane of small vesicles or thin tubules. The formation of these 'transport carriers' follows sequential events: membrane bending, fission from the donor compartment, transport and eventually fusion with the acceptor membrane. A similar sequence is involved during the internalization of drug or gene carriers inside cells. These membrane-shaping events are generally mediated by proteins binding to membranes. The mechanisms behind these biological processes are actively studied both in the context of cell biology and biophysics. Bin/amphiphysin/Rvs (BAR) domain proteins are ideally suited for illustrating how simple soft matter principles can account for membrane deformation by proteins. We review here some experimental methods and corresponding theoretical models to measure how these proteins affect the mechanics and the shape of membranes. In more detail, we show how an experimental method employing optical tweezers to pull a tube from a giant vesicle may give important quantitative insights into the mechanism by which proteins sense and generate membrane curvature and the mechanism of membrane scission.This article is part of the themed issue 'Soft interfacial materials: from fundamentals to formulation'.
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Affiliation(s)
- Mijo Simunovic
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Coline Prévost
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France
| | - Andrew Callan-Jones
- Laboratoire Matière et Systèmes Complexes, CNRS, UMR 7057, 75205 Paris Cedex 13, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France
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