1
|
Liebl K, Voth GA. Lipid Organization by the Caveolin-1 Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602986. [PMID: 39026816 PMCID: PMC11257593 DOI: 10.1101/2024.07.10.602986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Caveolins are lipid-binding proteins that can organize membrane remodeling and oligomerize into the 8S-complex. The CAV1 8S-complex comprises a disk-like structure, about 15nm in diameter, with a central beta barrel. Further oligomerization of 8S-complexes remodels the membrane into caveolae vessels, with a dependence on cholesterol concentration. However, the molecular mechanisms behind membrane remodeling and cholesterol filtering are still not understood. Performing atomistic Molecular Dynamics simulations in combination with advanced sampling techniques, we describe how the CAV1-8S complex bends the membrane and accumulates cholesterol. Here, our simulations show an enhancing effect by the palmitoylations of CAV1, and we predict that the CAV1-8S complex can extract cholesterol molecules from the lipid bilayer and accommodate them in its beta barrel. Through backmapping to the all-atom level we also conclude that the Martini v2 coarse-grained forcefield overestimates membrane bending, as the atomistic simulations exhibit only very localized bending.
Collapse
Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
2
|
Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions. J Membr Biol 2022; 255:651-663. [PMID: 35930019 PMCID: PMC9718270 DOI: 10.1007/s00232-022-00256-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
The plasma membrane (PM) of cells is a dynamic structure whose morphology and composition is in constant flux. PM morphologic changes are particularly relevant for the assembly and disassembly of signaling platforms involving surface-bound signaling proteins, as well as for many other mechanochemical processes that occur at the PM surface. Surface-bound membrane proteins (SBMP) require efficient association with the PM for their function, which is often achieved by the coordinated interactions of intrinsically disordered regions (IDRs) and globular domains with membrane lipids. This review focuses on the role of IDR-containing SBMPs in remodeling the composition and curvature of the PM. The ability of IDR-bearing SBMPs to remodel the Gaussian and mean curvature energies of the PM is intimately linked to their ability to sort subsets of phospholipids into nanoclusters. We therefore discuss how IDRs of many SBMPs encode lipid-binding specificity or facilitate cluster formation, both of which increase their membrane remodeling capacity, and how SBMP oligomers alter membrane shape by monolayer surface area expansion and molecular crowding.
Collapse
|
3
|
Tourdot RW, Ramakrishnan N, Parihar K, Radhakrishnan R. Quantification of Curvature Sensing Behavior of Curvature-Inducing Proteins on Model Wavy Substrates. J Membr Biol 2022; 255:175-184. [PMID: 35333976 DOI: 10.1007/s00232-022-00228-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 12/29/2022]
Abstract
Curvature-inducing proteins are involved in a variety of membrane remodeling processes in the cell. Several in vitro experiments have quantified the curvature sensing behavior of these proteins in model lipid systems. One such system consists of a membrane bilayer laid atop a wavy substrate (Hsieh in Langmuir 28:12838-12843, 2012). In these experiments, the bilayer conforms to the wavy substrate, and curvature-inducing proteins show preferential segregation on the wavy membrane. Using a mesoscale computational membrane model based on the Helfrich Hamiltonian, here we present a study which analyzes the curvature sensing characteristics of this membrane-protein system, and elucidates key physical principles governing protein segregation on the wavy substrate and other in vitro systems. In this article we compute the local protein densities from the free energy landscape associated with membrane remodeling by curvature-inducing proteins. In specific, we use the Widom insertion technique to compute the free energy landscape for an inhomogeneous system with spatially varying density and the results obtained with this minimal model show excellent agreement with experimental studies that demonstrate the association between membrane curvature and local protein density. The free energy-based framework employed in this study can be used for different membrane morphologies and varied protein characteristics to gain mechanistic insights into protein sorting on membranes.
Collapse
Affiliation(s)
- Richard W Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
4
|
Andersen RC, Schmidt JH, Rombach J, Lycas MD, Christensen NR, Lund VK, Stapleton DS, Pedersen SS, Olsen MA, Stoklund M, Noes-Holt G, Nielsen TT, Keller MP, Jansen AM, Herlo R, Pietropaolo M, Simonsen JB, Kjærulff O, Holst B, Attie AD, Gether U, Madsen KL. Coding variants identified in diabetic patients alter PICK1 BAR domain function in insulin granule biogenesis. J Clin Invest 2022; 132:144904. [PMID: 35077398 PMCID: PMC8884907 DOI: 10.1172/jci144904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Bin/amphiphysin/Rvs (BAR) domains are positively charged crescent-shaped modules that mediate curvature of negatively charged lipid membranes during remodeling processes. The BAR domain proteins PICK1, ICA69, and the arfaptins have recently been demonstrated to coordinate the budding and formation of immature secretory granules (ISGs) at the trans-Golgi network. Here, we identify 4 coding variants in the PICK1 gene from a whole-exome screening of Danish patients with diabetes that each involve a change in positively charged residues in the PICK1 BAR domain. All 4 coding variants failed to rescue insulin content in INS-1E cells upon knock down of endogenous PICK1. Moreover, 2 variants showed dominant-negative properties. In vitro assays addressing BAR domain function suggested that the coding variants compromised BAR domain function but increased the capacity to cause fission of liposomes. Live confocal microscopy and super-resolution microscopy further revealed that PICK1 resides transiently on ISGs before egress via vesicular budding events. Interestingly, this egress of PICK1 was accelerated in the coding variants. We propose that PICK1 assists in or complements the removal of excess membrane and generic membrane trafficking proteins, and possibly also insulin, from ISGs during the maturation process; and that the coding variants may cause premature budding, possibly explaining their dominant-negative function.
Collapse
Affiliation(s)
- Rita C. Andersen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan H. Schmidt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joscha Rombach
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Lycas
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaj R. Christensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor K. Lund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Signe S. Pedersen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias A. Olsen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Stoklund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gith Noes-Holt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tommas T.E. Nielsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Anna M. Jansen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Herlo
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Massimo Pietropaolo
- Diabetes Research Center, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jens B. Simonsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Kjærulff
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L. Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Sadeghi M, Noé F. Thermodynamics and Kinetics of Aggregation of Flexible Peripheral Membrane Proteins. J Phys Chem Lett 2021; 12:10497-10504. [PMID: 34677984 DOI: 10.1021/acs.jpclett.1c02954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomembrane remodeling is essential for cellular trafficking, with membrane-binding peripheral proteins playing a key role in it. Significant membrane remodeling as in endo- and exocytosis is often due to aggregates of many proteins with direct or membrane-mediated interactions. Understanding this process via computer simulations is extremely challenging: protein-membrane systems involve time and length scales that make atomistic simulations impractical, while most coarse-grained models fall short in resolving dynamics and physical effects of protein and membrane flexibility. Here, we develop a coarse-grained model of the bilayer membrane bestrewed with rotationally symmetric flexible proteins, parametrized to reflect local curvatures and lateral dynamics of proteins. We investigate the kinetics, equilibrium distributions, and the free energy landscape governing the formation and breakup of protein clusters on the surface of the membrane. We demonstrate how the flexibility of the proteins as well as their surface concentration play deciding roles in highly selective macroscopic aggregation behavior.
Collapse
Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany
| |
Collapse
|
7
|
Phillips DA, Zacharoff LA, Hampton CM, Chong GW, Malanoski AP, Metskas LA, Xu S, Bird LJ, Eddie BJ, Miklos AE, Jensen GJ, Drummy LF, El-Naggar MY, Glaven SM. A bacterial membrane sculpting protein with BAR domain-like activity. eLife 2021; 10:60049. [PMID: 34643180 PMCID: PMC8687657 DOI: 10.7554/elife.60049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.
Collapse
Affiliation(s)
- Daniel A Phillips
- Oak Ridge Institute for Science and Education / US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Cheri M Hampton
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Grace W Chong
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Lauren Ann Metskas
- Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
| | - Shuai Xu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Lina J Bird
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Aleksandr E Miklos
- BioSciences Division, BioChemistry Branch, US Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, United States
| | - Grant J Jensen
- Biology and Bioengineering, California Institute of Technology, Pasadena, United States
| | - Lawrence F Drummy
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| |
Collapse
|
8
|
Kim S, Voth GA. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J Phys Chem B 2021; 125:6874-6888. [PMID: 34139844 DOI: 10.1021/acs.jpcb.1c03559] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipid droplets (LDs) are neutral lipid-storing organelles surrounded by a phospholipid (PL) monolayer. At present, how LDs are formed in the endoplasmic reticulum (ER) bilayer is poorly understood. In this study, we present a revised all-atom (AA) triolein (TG) model, the main constituent of the LD core, and characterize its properties in a bilayer membrane to demonstrate the implications of its behavior in LD biogenesis. In bilayer simulations, TG resides at the surface, adopting PL-like conformations (denoted in this work as SURF-TG). Free energy sampling simulation results estimate the barrier for TG relocating from the bilayer surface to the bilayer center to be ∼2 kcal/mol in the absence of an oil lens. SURF-TG is able to modulate membrane properties by increasing PL ordering, decreasing bending modulus, and creating local negative curvature. The other neutral lipid, dioleoyl-glycerol (DAG), also reduces the membrane bending modulus and populates negative curvature regions. A phenomenological coarse-grained (CG) model is also developed to observe larger-scale SURF-TG-mediated membrane deformation. CG simulations confirm that TG nucleates between the bilayer leaflets at a critical concentration when SURF-TG is evenly distributed. However, when one monolayer contains more SURF-TG, the membrane bends toward the other leaflet, followed by TG nucleation if a concentration is higher than the critical threshold. The central conclusion of this study is that SURF-TG is a negative curvature inducer, as well as a membrane modulator. To this end, a model is proposed in which the accumulation of SURF-TG in the luminal leaflet bends the ER bilayer toward the cytosolic side, followed by TG nucleation.
Collapse
Affiliation(s)
- Siyoung Kim
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
9
|
Kandy SK, Janmey PA, Radhakrishnan R. Membrane signalosome: where biophysics meets systems biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 25:34-41. [PMID: 33997528 PMCID: PMC8117111 DOI: 10.1016/j.coisb.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We opine on the recent advances in experiments and modeling of modular signaling complexes assembled on mammalian cell membranes (membrane signalosomes) in the context of several applications including intracellular trafficking, cell migration, and immune response. Characterizing the individual components of the membrane assemblies at the nanoscale, ranging from protein-lipid and protein-protein interactions, to membrane morphology, and the energetics of emergent assemblies at the subcellular to cellular scales pose significant challenges. Overcoming these challenges through the iterative coupling of multiscale modeling and experiment can be transformative in terms of addressing the gaps between structural biology and super-resolution microscopy, as it holds the key to the discovery of fundamental mechanisms behind the emergence of function in the membrane signalosome.
Collapse
Affiliation(s)
- Sreeja K Kandy
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
| | - Paul A Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
10
|
Randolph PS, Stagg SM. Reconstruction of Average Subtracted Tubular Regions (RASTR) enables structure determination of tubular filaments by cryo-EM. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100023. [PMID: 32647826 PMCID: PMC7337063 DOI: 10.1016/j.yjsbx.2020.100023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/14/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Tubules (filaments, membrane tubules, etc) that stray from perfect symmetry or have decorations can be difficult to process. New method Reconstruction of Average Subtracted Tubular Regions (RASTR), provides a way to isolate small areas of tubular architecture. Upweighted and masked areas can be treated as single particles and the structure can be resolved using conventional refinement. Successfully reconstructed protein filaments and membrane tubule decorations.
As the field of electron microscopy advances, the increasing complexity of samples being produced demand more involved processing methods. In this study, we have developed a new processing method for generating 3D reconstructions of tubular structures. Tubular biomolecules are common throughout many cellular processes and are appealing targets for biophysical research. Processing of tubules with helical symmetry is relatively straightforward for electron microscopy if the helical parameters are known, but tubular structures that deviate from helical symmetry (asymmetrical components, local but no global order, etc) present myriad issues. Here we present a new processing technique called Reconstruction of Average Subtracted Tubular Regions (RASTR), which was developed to reconstruct tubular structures without applying symmetry. We explain the RASTR approach and quantify its performance using three examples: a simulated symmetrical tubular filament, a symmetrical tubular filament from cryo-EM data, and a membrane tubule coated with locally ordered but not globally ordered proteins.
Collapse
Affiliation(s)
- Peter S Randolph
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
11
|
Gowrisankaran S, Wang Z, Morgan DG, Milosevic I, Mim C. Cells Control BIN1-Mediated Membrane Tubulation by Altering the Membrane Charge. J Mol Biol 2019; 432:1235-1250. [PMID: 31857086 DOI: 10.1016/j.jmb.2019.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/18/2019] [Accepted: 12/07/2019] [Indexed: 11/15/2022]
Abstract
The Bridging integrator 1 (BIN1)/Amphiphysin/Rvs (BAR) protein family is an essential part of the cell's machinery to bend membranes. BIN1 is a muscle-enriched BAR protein with an established role in muscle development and skeletal myopathies. Here, we demonstrate that BIN1, on its own, is able to form complex interconnected tubular systems in vitro, reminiscent of t-tubule system in muscle cells. We further describe how BIN1's electrostatic interactions regulate membrane bending: the ratio of negatively charged lipids in the bilayer altered membrane bending and binding properties of BIN1 and so did the manipulation of BIN1's surface charge. We show that the electrostatically mediated BIN1 membrane binding depended on the membrane curvature-it was less affected in liposomes with high curvature. Curiously, BIN1 membrane binding and bending was diminished in cells where the membrane's charge was experimentally reduced. Membrane bending was also reduced in BIN1 mutants where negative or positive charges in the BAR domain have been eliminated. This phenotype, characteristic of BIN1 mutants linked to myopathies, was rescued when the membrane charge was made more negative. The latter findings also show that cells can control tubulation at their membranes by simply altering the membrane charge and through it, the recruitment of BAR proteins and their interaction partners (e.g. dynamin).
Collapse
Affiliation(s)
- Sindhuja Gowrisankaran
- European Neuroscience Institute (ENI), A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society, Synaptic Vesicle Dynamics Group, Göttingen, Germany
| | - Zuoneng Wang
- Royal Technical Institute (KTH), Dept. for Biomedical Engineering and Health Systems, Stockholm, Sweden; Karolinska Institute, Department of Nutrition and Biosciences, Huddinge, Sweden
| | - David G Morgan
- Indiana University, Electron Microscopy Center, Bloomington, IN USA
| | - Ira Milosevic
- European Neuroscience Institute (ENI), A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society, Synaptic Vesicle Dynamics Group, Göttingen, Germany
| | - Carsten Mim
- Royal Technical Institute (KTH), Dept. for Biomedical Engineering and Health Systems, Stockholm, Sweden; Karolinska Institute, Department of Nutrition and Biosciences, Huddinge, Sweden.
| |
Collapse
|
12
|
Rahman MM, Ueda M, Son K, Seo S, Takeoka S, Hirose T, Ito Y. Tubular Network Formation by Mixing Amphiphilic Polypeptides with Differing Hydrophilic Blocks. Biomacromolecules 2019; 20:3908-3914. [PMID: 31532187 DOI: 10.1021/acs.biomac.9b00986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Artificial tubular networks are promising structures for biomaterial applications because of their large surface areas. A tubular network was formed by co-assembling two different amphiphilic polypeptides, poly(ethylene glycol)-b-(l-Leu-Aib)6 (PL12) and polysarcosine-b-(l-Leu-Aib)6 (SL12). They both have the same hydrophobic 12-mer helical block (l-Leu-Aib)6 but different hydrophilic chains, poly(ethylene glycol) and polysarcosine. In water, both polypeptides self-assembled into a tubular structure having a uniform 80 nm diameter that was formed by packing among the hydrophobic L12 blocks. The SL12 nanotubes were short (200 nm), straight, and robust. PL12 formed long (>1 μm), bendable, and fusogenic nanotubes. The amphiphiles were then co-assembled with various mixing ratios to form tubular networks. Higher concentrations of PL12 made the nanotubes more bendable and fusogenic between open tube ends, which produced branching junctions under heat treatment.
Collapse
Affiliation(s)
- Md Mofizur Rahman
- Emergent Bioengineering Materials Research Team , RIKEN Center for Emergent Matter Science (CEMS) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Graduate School of Science and Engineering , Saitama University , 255 Shimo-Okubo , Sakura-ku, Saitama City , Saitama 338-8570 , Japan.,Faculty of Allied Health Sciences , Daffodil International University , 4/2, Sobhanbag , Mirpur Road , Dhaka 1207 , Bangladesh
| | - Motoki Ueda
- Emergent Bioengineering Materials Research Team , RIKEN Center for Emergent Matter Science (CEMS) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Nano Medical Engineering Laboratory , RIKEN Center for Pioneering Research (CPR) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan
| | - Kon Son
- Emergent Bioengineering Materials Research Team , RIKEN Center for Emergent Matter Science (CEMS) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Graduate School of Advanced Science and Engineering , Waseda University , 2-2 TWIns, Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 Japan
| | - Siyoong Seo
- Emergent Bioengineering Materials Research Team , RIKEN Center for Emergent Matter Science (CEMS) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan
| | - Shinji Takeoka
- Graduate School of Advanced Science and Engineering , Waseda University , 2-2 TWIns, Wakamatsu-cho , Shinjuku-ku, Tokyo 162-8480 Japan
| | - Takuji Hirose
- Graduate School of Science and Engineering , Saitama University , 255 Shimo-Okubo , Sakura-ku, Saitama City , Saitama 338-8570 , Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team , RIKEN Center for Emergent Matter Science (CEMS) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Nano Medical Engineering Laboratory , RIKEN Center for Pioneering Research (CPR) , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Le Roux AL, Quiroga X, Walani N, Arroyo M, Roca-Cusachs P. The plasma membrane as a mechanochemical transducer. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180221. [PMID: 31431176 PMCID: PMC6627014 DOI: 10.1098/rstb.2018.0221] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Cells are constantly submitted to external mechanical stresses, which they must withstand and respond to. By forming a physical boundary between cells and their environment that is also a biochemical platform, the plasma membrane (PM) is a key interface mediating both cellular response to mechanical stimuli, and subsequent biochemical responses. Here, we review the role of the PM as a mechanosensing structure. We first analyse how the PM responds to mechanical stresses, and then discuss how this mechanical response triggers downstream biochemical responses. The molecular players involved in PM mechanochemical transduction include sensors of membrane unfolding, membrane tension, membrane curvature or membrane domain rearrangement. These sensors trigger signalling cascades fundamental both in healthy scenarios and in diseases such as cancer, which cells harness to maintain integrity, keep or restore homeostasis and adapt to their external environment. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
Collapse
Affiliation(s)
- Anabel-Lise Le Roux
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Xarxa Quiroga
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Nikhil Walani
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Marino Arroyo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- Department of Biomedical Sciences, Universitat de Barcelona, Barcelona 08036, Spain
| |
Collapse
|
15
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
Collapse
Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
16
|
Bhattacharya S, Phatake RS, Nabha Barnea S, Zerby N, Zhu JJ, Shikler R, Lemcoff NG, Jelinek R. Fluorescent Self-Healing Carbon Dot/Polymer Gels. ACS NANO 2019; 13:7396-7401. [PMID: 30615415 DOI: 10.1021/acsnano.9b05112] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Multicolor, fluorescent self-healing gels were constructed through reacting carbon dots produced from different aldehyde precursors with branched polyethylenimine. The self-healing gels were formed through Schiff base reaction between the aldehyde units displayed upon the carbon dots' surface and primary amine residues within the polyethylenimine network, generating imine bonds. The dynamic covalent imine bonds between the carbon dots and polymeric matrix endowed the gels with both excellent self-healing properties as well as high mechanical strength. Moreover, the viscoelastic properties of the gels could be intimately modulated by controlling the ratio between the carbon dots and polymer. The distinct fluorescence emissions of the gels, originating from the specific carbon dot constituents, were employed for fabrication of light emitters at different colors, particularly generating white light.
Collapse
Affiliation(s)
- Sagarika Bhattacharya
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | | | - Shiran Nabha Barnea
- Department of Electrical and Computer Engineering , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Nicholas Zerby
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Rafi Shikler
- Department of Electrical and Computer Engineering , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Norberto Gabriel Lemcoff
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
- Ilse Katz Institute for Nanotechnology , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Raz Jelinek
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
- Ilse Katz Institute for Nanotechnology , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| |
Collapse
|
17
|
Ader NR, Hoffmann PC, Ganeva I, Borgeaud AC, Wang C, Youle RJ, Kukulski W. Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis. eLife 2019; 8:40712. [PMID: 30714902 PMCID: PMC6361589 DOI: 10.7554/elife.40712] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing it. However, it remains unclear how outer membrane openings form. Here, we combined different correlative microscopy and electron cryo-tomography approaches to visualize the effects of Bax activity on mitochondria in human cells. Our data show that Bax clusters localize near outer membrane ruptures of highly variable size. Bax clusters contain structural elements suggesting a higher order organization of their components. Furthermore, unfolding of inner membrane cristae is coupled to changes in the supramolecular assembly of ATP synthases, particularly pronounced at membrane segments exposed to the cytosol by ruptures. Based on our results, we propose a comprehensive model in which molecular reorganizations of the inner membrane and sequestration of outer membrane components into Bax clusters interplay in the formation of outer membrane ruptures. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Collapse
Affiliation(s)
- Nicholas R Ader
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Iva Ganeva
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alicia C Borgeaud
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
18
|
Machado S, Mercier V, Chiaruttini N. LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation. BMC Bioinformatics 2019; 20:2. [PMID: 30606118 PMCID: PMC6318983 DOI: 10.1186/s12859-018-2471-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/06/2018] [Indexed: 11/15/2022] Open
Abstract
Background 3D segmentation is often a prerequisite for 3D object display and quantitative measurements. Yet existing voxel-based methods do not directly give information on the object surface or topology. As for spatially continuous approaches such as level-set, active contours and meshes, although providing surfaces and concise shape description, they are generally not suitable for multiple object segmentation and/or for objects with an irregular shape, which can hamper their adoption by bioimage analysts. Results We developed LimeSeg, a computationally efficient and spatially continuous 3D segmentation method. LimeSeg is easy-to-use and can process many and/or highly convoluted objects. Based on the concept of SURFace ELements (“Surfels”), LimeSeg resembles a highly coarse-grained simulation of a lipid membrane in which a set of particles, analogous to lipid molecules, are attracted to local image maxima. The particles are self-generating and self-destructing thus providing the ability for the membrane to evolve towards the contour of the objects of interest. The capabilities of LimeSeg: simultaneous segmentation of numerous non overlapping objects, segmentation of highly convoluted objects and robustness for big datasets are demonstrated on experimental use cases (epithelial cells, brain MRI and FIB-SEM dataset of cellular membrane system respectively). Conclusion In conclusion, we implemented a new and efficient 3D surface reconstruction plugin adapted for various sources of images, which is deployed in the user-friendly and well-known ImageJ environment.
Collapse
Affiliation(s)
- Sarah Machado
- Marcos González Gaitán lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, Geneva, 1211, Switzerland
| | - Vincent Mercier
- Aurélien Roux lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, Geneva, 1211, Switzerland
| | - Nicolas Chiaruttini
- Aurélien Roux lab, University of Geneva, Department of Biochemistry, quai Ernest-Ansermet 30, Geneva, 1211, Switzerland.
| |
Collapse
|
19
|
Rosquete MR, Drakakaki G. Plant TGN in the stress response: a compartmentalized overview. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:122-129. [PMID: 30316189 DOI: 10.1016/j.pbi.2018.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 05/10/2023]
Abstract
The cellular responses to abiotic and biotic stress rely on the regulation of vesicle trafficking to ensure the correct localization of proteins specialized in sensing stress stimuli and effecting the response. Several studies have implicated the plant trans-Golgi network (TGN)-mediated trafficking in different types of biotic and abiotic stress responses; however, the underlying molecular mechanisms are poorly understood. Further, the identity, specialization and stress-relevant cargo transported by the TGN subcompartments involved in stress responses await more in depth characterization. This review presents TGN trafficking players implicated in stress and discusses potential avenues to understand the role of this dynamic network under such extreme circumstances.
Collapse
Affiliation(s)
- Michel Ruiz Rosquete
- Department of Plant Sciences, University of California, Davis, CA 95616, United States.
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, CA 95616, United States.
| |
Collapse
|
20
|
BAR domain proteins-a linkage between cellular membranes, signaling pathways, and the actin cytoskeleton. Biophys Rev 2018; 10:1587-1604. [PMID: 30456600 DOI: 10.1007/s12551-018-0467-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
Actin filament assembly typically occurs in association with cellular membranes. A large number of proteins sit at the interface between actin networks and membranes, playing diverse roles such as initiation of actin polymerization, modulation of membrane curvature, and signaling. Bin/Amphiphysin/Rvs (BAR) domain proteins have been implicated in all of these functions. The BAR domain family of proteins comprises a diverse group of multi-functional effectors, characterized by their modular architecture. In addition to the membrane-curvature sensing/inducing BAR domain module, which also mediates antiparallel dimerization, most contain auxiliary domains implicated in protein-protein and/or protein-membrane interactions, including SH3, PX, PH, RhoGEF, and RhoGAP domains. The shape of the BAR domain itself varies, resulting in three major subfamilies: the classical crescent-shaped BAR, the more extended and less curved F-BAR, and the inverse curvature I-BAR subfamilies. Most members of this family have been implicated in cellular functions that require dynamic remodeling of the actin cytoskeleton, such as endocytosis, organelle trafficking, cell motility, and T-tubule biogenesis in muscle cells. Here, we review the structure and function of mammalian BAR domain proteins and the many ways in which they are interconnected with the actin cytoskeleton.
Collapse
|
21
|
Voth GA. Simulations of N-BAR Protein Interactions with Membranes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:35-36. [PMID: 32255841 PMCID: PMC7111462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
22
|
Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
Collapse
Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Bassereau P, Jin R, Baumgart T, Deserno M, Dimova R, Frolov VA, Bashkirov PV, Grubmüller H, Jahn R, Risselada HJ, Johannes L, Kozlov MM, Lipowsky R, Pucadyil TJ, Zeno WF, Stachowiak JC, Stamou D, Breuer A, Lauritsen L, Simon C, Sykes C, Voth GA, Weikl TR. The 2018 biomembrane curvature and remodeling roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:343001. [PMID: 30655651 PMCID: PMC6333427 DOI: 10.1088/1361-6463/aacb98] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds. On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo- and exocytosis, phagocytosis and filopodia formation. On the other hand, a multitude of intracellular processes at the level of organelles rely on generation, modulation, and maintenance of membrane curvature to maintain the organelle shape and functionality. The contribution of biophysicists and biologists is essential for shedding light on the mechanistic understanding and quantification of these processes. Given the vast complexity of phenomena and mechanisms involved in the coupling between membrane shape and function, it is not always clear in what direction to advance to eventually arrive at an exhaustive understanding of this important research area. The 2018 Biomembrane Curvature and Remodeling Roadmap of Journal of Physics D: Applied Physics addresses this need for clarity and is intended to provide guidance both for students who have just entered the field as well as established scientists who would like to improve their orientation within this fascinating area.
Collapse
Affiliation(s)
- Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Rui Jin
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Tobias Baumgart
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, United States of America
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - H Jelger Risselada
- Department of Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Michael M Kozlov
- Sackler Faculty of Medicine, Department of Physiology and Pharmacology, Tel Aviv University
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | | | - Wade F Zeno
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Austin, TX, United States of America
| | - Dimitrios Stamou
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Artú Breuer
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Line Lauritsen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Camille Simon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Cécile Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| |
Collapse
|
25
|
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.
Collapse
Affiliation(s)
- N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | | | | | | |
Collapse
|
26
|
Sadeghi M, Weikl TR, Noé F. Particle-based membrane model for mesoscopic simulation of cellular dynamics. J Chem Phys 2018; 148:044901. [PMID: 29390800 DOI: 10.1063/1.5009107] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.
Collapse
Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
|
29
|
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.
Collapse
Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan.
| |
Collapse
|
30
|
Manni MM, Derganc J, Čopič A. Crowd-Sourcing of Membrane Fission. Bioessays 2017; 39. [DOI: 10.1002/bies.201700117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Marco M. Manni
- Université Côte d'Azur; CNRS, IPMC; 06560 Valbonne France
| | - Jure Derganc
- Institute of Biophysics; Faculty of Medicine; University of Ljubljana; 1000 Ljubljana Slovenia
| | - Alenka Čopič
- Institut Jacques Monod, CNRS UMR 7592; Université Paris Diderot; Sorbonne Paris Cité 75013 Paris France
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Simunovic M, Manneville JB, Renard HF, Evergren E, Raghunathan K, Bhatia D, Kenworthy AK, Voth GA, Prost J, McMahon HT, Johannes L, Bassereau P, Callan-Jones A. Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins. Cell 2017. [PMID: 28648660 PMCID: PMC5576516 DOI: 10.1016/j.cell.2017.05.047] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Membrane scission is essential for intracellular trafficking. While BAR domain proteins such as endophilin have been reported in dynamin-independent scission of tubular membrane necks, the cutting mechanism has yet to be deciphered. Here, we combine a theoretical model, in vitro, and in vivo experiments revealing how protein scaffolds may cut tubular membranes. We demonstrate that the protein scaffold bound to the underlying tube creates a frictional barrier for lipid diffusion; tube elongation thus builds local membrane tension until the membrane undergoes scission through lysis. We call this mechanism friction-driven scission (FDS). In cells, motors pull tubes, particularly during endocytosis. Through reconstitution, we show that motors not only can pull out and extend protein-scaffolded tubes but also can cut them by FDS. FDS is generic, operating even in the absence of amphipathic helices in the BAR domain, and could in principle apply to any high-friction protein and membrane assembly.
Collapse
Affiliation(s)
- Mijo Simunovic
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC University Paris 06, 75005 Paris, France; Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Jean-Baptiste Manneville
- Subcellular Structure and Cellular Dynamics Unit, Institut Curie, PSL Research University, CNRS UMR144, 75005 Paris, France
| | - Henri-François Renard
- Chemical Biology of Membranes and Therapeutic Delivery Unit, Institut Curie, PSL Research University, CNRS UMR3666, INSERM U1143, 75005 Paris, France
| | - Emma Evergren
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Krishnan Raghunathan
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, 718 Light Hall, Nashville, TN 37232, USA
| | - Dhiraj Bhatia
- Chemical Biology of Membranes and Therapeutic Delivery Unit, Institut Curie, PSL Research University, CNRS UMR3666, INSERM U1143, 75005 Paris, France
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, 718 Light Hall, Nashville, TN 37232, USA
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Jacques Prost
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC University Paris 06, 75005 Paris, France; Mechanobiology Institute, National University of Singapore, Singapore 119077, Singapore
| | - Harvey T McMahon
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ludger Johannes
- Chemical Biology of Membranes and Therapeutic Delivery Unit, Institut Curie, PSL Research University, CNRS UMR3666, INSERM U1143, 75005 Paris, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France; Sorbonne Universités, UPMC University Paris 06, 75005 Paris, France.
| | - Andrew Callan-Jones
- Laboratoire Matière et Systèmes Complexes, CNRS UMR7057, 75205 Paris, France.
| |
Collapse
|
34
|
Czogalla A, Franquelim HG, Schwille P. DNA Nanostructures on Membranes as Tools for Synthetic Biology. Biophys J 2017; 110:1698-1707. [PMID: 27119630 PMCID: PMC4850321 DOI: 10.1016/j.bpj.2016.03.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/26/2015] [Accepted: 03/07/2016] [Indexed: 11/12/2022] Open
Abstract
Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.
Collapse
Affiliation(s)
- Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
35
|
Pizzirusso A, De Nicola A, Sevink GJA, Correa A, Cascella M, Kawakatsu T, Rocco M, Zhao Y, Celino M, Milano G. Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model. Phys Chem Chem Phys 2017; 19:29780-29794. [DOI: 10.1039/c7cp03871b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using hybrid particle field–self consistence field simulations.
Collapse
Affiliation(s)
| | - Antonio De Nicola
- Dipartimento di Chimica e Biologia
- Università di Salerno
- Fisciano
- Italy
| | - G. J. Agur Sevink
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden
- The Netherlands
| | - Andrea Correa
- Department of Chemical Science
- Federico II University of Naples
- 80126 Napoli
- Italy
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences
- University of Oslo
- 0371 Oslo
- Norway
| | | | - Mattia Rocco
- Biopolimeri e Proteomica
- Ospedale Policlinico San Martino
- Genova
- Italy
| | - Ying Zhao
- Institute of Nano-Photonics
- School of Physics and Materials Engineering
- Dalian Minzu University
- Dalian 116600
- China
| | | | - Giuseppe Milano
- Dipartimento di Chimica e Biologia
- Università di Salerno
- Fisciano
- Italy
| |
Collapse
|
36
|
Dan N. Membrane-induced interactions between curvature-generating protein domains: the role of area perturbation. AIMS BIOPHYSICS 2017. [DOI: 10.3934/biophy.2017.1.107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
37
|
Zhu X, Gojgini S, Chen TH, Teng F, Fei P, Dong S, Segura T, Ho CM. Three dimensional tubular structure self-assembled by vascular mesenchymal cells at stiffness interfaces of hydrogels. Biomed Pharmacother 2016; 83:1203-1211. [DOI: 10.1016/j.biopha.2016.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/26/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022] Open
|
38
|
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.
Collapse
|
39
|
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'.
Collapse
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
| |
Collapse
|
40
|
Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
Collapse
|
41
|
Noguchi H. Shape deformation of lipid membranes by banana-shaped protein rods: Comparison with isotropic inclusions and membrane rupture. Phys Rev E 2016; 93:052404. [PMID: 27300921 DOI: 10.1103/physreve.93.052404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Indexed: 06/06/2023]
Abstract
The assembly of curved protein rods on fluid membranes is studied using implicit-solvent meshless membrane simulations. As the rod curvature increases, the rods on a membrane tube assemble along the azimuthal direction first and subsequently along the longitudinal direction. Here, we show that both transition curvatures decrease with increasing rod stiffness. For comparison, curvature-inducing isotropic inclusions are also simulated. When the isotropic inclusions have the same bending rigidity as the other membrane regions, the inclusions are uniformly distributed on the membrane tubes and vesicles even for large spontaneous curvature of the inclusions. However, the isotropic inclusions with much larger bending rigidity induce shape deformation and are concentrated on the region of a preferred curvature. For high rod density, high rod stiffness, and/or low line tension of the membrane edge, the rod assembly induces vesicle rupture, resulting in the formation of a high-genus vesicle. A gradual change in the curvature suppresses this rupture. Hence, large stress, compared to the edge tension, induced by the rod assembly is the key factor determining rupture. For rod curvature with the opposite sign to the vesicle curvature, membrane rupture induces inversion of the membrane, leading to division into multiple vesicles as well as formation of a high-genus vesicle.
Collapse
Affiliation(s)
- Hiroshi Noguchi
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
42
|
Simunovic M, Voth GA, Callan-Jones A, Bassereau P. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol 2015; 25:780-792. [PMID: 26519988 DOI: 10.1016/j.tcb.2015.09.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 10/22/2022]
Abstract
Cell membranes become highly curved during membrane trafficking, cytokinesis, infection, immune response, or cell motion. Bin/amphiphysin/Rvs (BAR) domain proteins with their intrinsically curved and anisotropic shape are involved in many of these processes, but with a large spectrum of modes of action. In vitro experiments and multiscale computer simulations have contributed in identifying a minimal set of physical parameters, namely protein density on the membrane, membrane tension, and membrane shape, that control how bound BAR domain proteins behave on the membrane. In this review, we summarize the multifaceted coupling of BAR proteins to membrane mechanics and propose a simple phase diagram that recapitulates the effects of these parameters.
Collapse
Affiliation(s)
- Mijo Simunovic
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, 5735 S Ellis Avenue, Chicago, IL 60637, USA; Institut Curie, Centre de Recherche, F-75248 Paris, France
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute and Computation Institute, The University of Chicago, 5735 S Ellis Avenue, Chicago, IL 60637, USA
| | - Andrew Callan-Jones
- Université Paris Diderot, F-75205 Paris, France; CNRS, Matière et Systèmes Complexes, UMR 7057, F-75205 Paris, France
| | - Patricia Bassereau
- Institut Curie, Centre de Recherche, F-75248 Paris, France; CNRS, PhysicoChimie Curie, UMR 168, F-75248 Paris, France; Université Pierre et Marie Curie, F-75252 Paris, France.
| |
Collapse
|
43
|
Membrane tension controls the assembly of curvature-generating proteins. Nat Commun 2015; 6:7219. [PMID: 26008710 PMCID: PMC4455092 DOI: 10.1038/ncomms8219] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/18/2015] [Indexed: 12/16/2022] Open
Abstract
Proteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane curvature in the cell. Recent simulations have revealed that BAR proteins assemble into linear aggregates, strongly affecting membrane curvature and its in-plane stress profile. Here, we explore the opposite question: do mechanical properties of the membrane impact protein association? By using coarse-grained molecular dynamics simulations, we show that increased surface tension significantly impacts the dynamics of protein assembly. While tensionless membranes promote a rapid formation of long-living linear aggregates of N-BAR proteins, increase in tension alters the geometry of protein association. At high tension, protein interactions are strongly inhibited. Increasing surface density of proteins leads to a wider range of protein association geometries, promoting the formation of meshes, which can be broken apart with membrane tension. Our work indicates that surface tension may play a key role in recruiting proteins to membrane-remodelling sites in the cell. BAR domain proteins are known to reshape cell membranes. Using coarse-grained molecular dynamics simulations, Simunovic and Voth demonstrate that membrane tension strongly affects the association of BAR proteins, in turn controlling their recruitment to membrane-remodelling sites.
Collapse
|
44
|
Czogalla A, Kauert DJ, Franquelim HG, Uzunova V, Zhang Y, Seidel R, Schwille P. Amphipathic DNA Origami Nanoparticles to Scaffold and Deform Lipid Membrane Vesicles. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501173] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
45
|
Czogalla A, Kauert DJ, Franquelim HG, Uzunova V, Zhang Y, Seidel R, Schwille P. Amphipathic DNA origami nanoparticles to scaffold and deform lipid membrane vesicles. Angew Chem Int Ed Engl 2015; 54:6501-5. [PMID: 25882792 DOI: 10.1002/anie.201501173] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/13/2015] [Indexed: 01/20/2023]
Abstract
We report a synthetic biology-inspired approach for the engineering of amphipathic DNA origami structures as membrane-scaffolding tools. The structures have a flat membrane-binding interface decorated with cholesterol-derived anchors. Sticky oligonucleotide overhangs on their side facets enable lateral interactions leading to the formation of ordered arrays on the membrane. Such a tight and regular arrangement makes our DNA origami capable of deforming free-standing lipid membranes, mimicking the biological activity of coat-forming proteins, for example, from the I-/F-BAR family.
Collapse
Affiliation(s)
- Aleksander Czogalla
- Biotechnology Center of the TU Dresden, Tatzberg 47/51, 01307 Dresden (Germany).,Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław ul. F. Joliot-Curie 14a, 50383 Wrocław (Poland)
| | - Dominik J Kauert
- Institute for Molecular Cell Biology, University of Münster, Schlossplatz 5, 48149 Münster (Germany)
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany) http://www.biochem.mpg.de/en/rd/schwille/
| | - Veselina Uzunova
- B CUBE-Center for Molecular Bioengineering, Dresden, University of Technology, Arnoldstraße 18, 01307 Dresden (Germany)
| | - Yixin Zhang
- B CUBE-Center for Molecular Bioengineering, Dresden, University of Technology, Arnoldstraße 18, 01307 Dresden (Germany)
| | - Ralf Seidel
- Institute for Molecular Cell Biology, University of Münster, Schlossplatz 5, 48149 Münster (Germany)
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany) http://www.biochem.mpg.de/en/rd/schwille/.
| |
Collapse
|
46
|
Molecular dynamics simulations of large macromolecular complexes. Curr Opin Struct Biol 2015; 31:64-74. [PMID: 25845770 DOI: 10.1016/j.sbi.2015.03.007] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/11/2022]
Abstract
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.
Collapse
|
47
|
Morriss-Andrews A, Shea JE. Computational Studies of Protein Aggregation: Methods and Applications. Annu Rev Phys Chem 2015; 66:643-66. [DOI: 10.1146/annurev-physchem-040513-103738] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joan-Emma Shea
- Department of Physics and
- Department of Chemistry, University of California, Santa Barbara, California 93106;
| |
Collapse
|
48
|
Ramakrishnan N, Ipsen JH, Rao M, Kumar PBS. Organelle morphogenesis by active membrane remodeling. SOFT MATTER 2015; 11:2387-2393. [PMID: 25672939 DOI: 10.1039/c4sm02311k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate, through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and composition segregation in closed membranes. We find that the steady state shapes obtained as a result of such active processes, bear a striking resemblance to the ramified morphologies of organelles in vivo, pointing to the relevance of nonequilibrium fission-fusion in organelle morphogenesis.
Collapse
Affiliation(s)
- N Ramakrishnan
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India.
| | | | | | | |
Collapse
|
49
|
Czogalla A, Kauert DJ, Seidel R, Schwille P, Petrov EP. DNA origami nanoneedles on freestanding lipid membranes as a tool to observe isotropic-nematic transition in two dimensions. NANO LETTERS 2015; 15:649-55. [PMID: 25467421 DOI: 10.1021/nl504158h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We introduce a simple experimental system to study dynamics of needle-like nanoobjects in two dimensions (2D) as a function of their surface density close to the isotropic-nematic transition. Using fluorescence correlation spectroscopy, we find that translational and rotational diffusion of rigid DNA origami nanoneedles bound to freestanding lipid membranes is strongly suppressed upon an increase in the surface particle density. Our experimental observations show a good agreement with results of Monte Carlo simulations of Brownian hard needles in 2D.
Collapse
Affiliation(s)
- Aleksander Czogalla
- Laboratory of Membrane Biochemistry, Paul Langerhans Institute, Technische Universität Dresden , Fetscherstraße 74, 01307 Dresden, Germany
| | | | | | | | | |
Collapse
|
50
|
Ramakrishnan N, Radhakrishnan R. Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies. ACTA ACUST UNITED AC 2015; 22:129-175. [PMID: 27087801 DOI: 10.1016/bs.adplan.2015.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intriguing question in cell biology is "how do cells regulate their shape?" It is commonly believed that the observed cellular morphologies are a result of the complex interaction among the lipid molecules (constituting the cell membrane), and with a number of other macromolecules, such as proteins. It is also believed that the common biophysical processes essential for the functioning of a cell also play an important role in cellular morphogenesis. At the cellular scale-where typical dimensions are in the order of micrometers-the effects arising from the molecular scale can either be modeled as equilibrium or non-equilibrium processes. In this chapter, we discuss the dynamically triangulated Monte Carlo technique to model and simulate membrane morphologies at the cellular scale, which in turn can be used to investigate several questions related to shape regulation in cells. In particular, we focus on two specific problems within the framework of isotropic and anisotropic elasticity theories: namely, (i) the origin of complex, physiologically relevant, membrane shapes due to the interaction of the membrane with curvature remodeling proteins, and (ii) the genesis of steady state cellular shapes due to the action of non-equilibrium forces that are generated by the fission and fusion of transport vesicles and by the binding and unbinding of proteins from the parent membrane.
Collapse
Affiliation(s)
- N Ramakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
| |
Collapse
|