1
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He W, Kirmizialtin S. Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations. Biomacromolecules 2024; 25:4819-4830. [PMID: 39011747 PMCID: PMC11323003 DOI: 10.1021/acs.biomac.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, the mechanisms of DNA assembly in lipid bilayers remain insufficiently understood due to challenges in measuring and assessing each component's contribution in the lipid-DNA-cation system. This study uses all-atom molecular dynamics simulations to investigate DNA condensation in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between lipid and DNA drastically reduce charges, while mobile magnesium cations "ping-ponging" between double strands create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the spontaneous condensation of DNAs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.
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Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
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2
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Sakuma Y, Kayamori N, Tanaka J, Haga K, Imai M, Kawakatsu T. Effects of grafted polymers on the lipid membrane fluidity. Biophys J 2024; 123:489-501. [PMID: 38243595 PMCID: PMC10912922 DOI: 10.1016/j.bpj.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/27/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
Since the membrane fluidity controls the cellular functions, it is important to identify the factors that determine the cell membrane viscosity. Cell membranes are composed of not only lipids and proteins but also polysaccharide chain-anchored molecules, such as glycolipids. To reveal the effects of grafted polymers on the membrane fluidity, in this study, we measured the membrane viscosity of polymer-grafted giant unilamellar vesicles (GUVs), which were prepared by introducing the poly (ethylene glycol) (PEG)-anchored lipids to the ternary GUVs composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol. The membrane viscosity was obtained from the velocity field on the GUV generated by applying a point force, based on the hydrodynamic model proposed by Henle and Levine. The velocity field was visualized by a motion of the circular liquid ordered (Lo) domains formed by a phase separation. With increasing PEG density, the membrane viscosity of PEG-grafted GUVs increased gradually in the mushroom region and significantly in the brush region. We propose a hydrodynamic model that includes the excluded volume effect of PEG chains to explain the increase in membrane viscosity in the mushroom region. This work provides a basic understanding of how grafted polymers affect the membrane fluidity.
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Affiliation(s)
- Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan.
| | - Nana Kayamori
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Julia Tanaka
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Kenya Haga
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
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3
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Liu P, Beltramo PJ. Effects of crowding on the diffusivity of membrane adhered particles. SOFT MATTER 2023; 19:7708-7716. [PMID: 37791427 DOI: 10.1039/d3sm01269g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation of complexes, cell-cell signaling, and membrane trafficking. These diffusive processes are complicated by how concentrated, or "crowded", the inclusions are, which can occupy between 30-50% of the area fraction of the membrane. In this work, we elucidate the effects of increasing concentration of model membrane inclusions in a free-standing artificial cell membrane on inclusion diffusivity and the apparent viscosity of the membrane. By multiple particle tracking of fluorescent microparticles covalently tethered to the bilayer, we show the transition from expected Brownian dynamics, which accurately measure the membrane viscosity, to subdiffusive behavior with decreased diffusion coefficient as the particle area fraction increases from 1% to around 30%, approaching physiological levels of crowding. At high crowding, the onset of non-Gaussian behavior is observed. Using hydrodynamic models relating the 2D diffusion coefficient to the viscosity of a membrane, we determine the apparent viscosity of the bilayer from the particle diffusivity and show an increase in the apparent membrane viscosity with increasing particle area fraction. However, the scaling of this increase is in contrast with the behavior of monolayer inclusion diffusion and bulk suspension rheology. These results demonstrate that physiological levels of model membrane crowding nontrivially alter the dynamics and apparent viscosity of the system, which has implications for understanding membrane protein interactions and particle-membrane transport processes.
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Affiliation(s)
- Paige Liu
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Peter J Beltramo
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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4
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Chawla R, Tom JKA, Boyd T, Grotjahn DA, Park D, Deniz AA, Racki LR. Reentrant DNA shells tune polyphosphate condensate size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557044. [PMID: 37745474 PMCID: PMC10515899 DOI: 10.1101/2023.09.13.557044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The ancient, inorganic biopolymer polyphosphate (polyP) occurs in all three domains of life and affects myriad cellular processes. An intriguing feature of polyP is its frequent proximity to chromatin, and in the case of many bacteria, its occurrence in the form of magnesium-enriched condensates embedded in the nucleoid, particularly in response to stress. The physical basis of the interaction between polyP and DNA, two fundamental anionic biopolymers, and the resulting effects on the organization of both the nucleoid and polyP condensates remain poorly understood. Given the essential role of magnesium ions in the coordination of polymeric phosphate species, we hypothesized that a minimal system of polyP, magnesium ions, and DNA (polyP-Mg2+-DNA) would capture key features of the interplay between the condensates and bacterial chromatin. We find that DNA can profoundly affect polyP-Mg2+ coacervation even at concentrations several orders of magnitude lower than found in the cell. The DNA forms shells around polyP-Mg2+ condensates and these shells show reentrant behavior, primarily forming in the concentration range close to polyP-Mg2+ charge neutralization. This surface association tunes both condensate size and DNA morphology in a manner dependent on DNA properties, including length and concentration. Our work identifies three components that could form the basis of a central and tunable interaction hub that interfaces with cellular interactors. These studies will inform future efforts to understand the basis of polyP granule composition and consolidation, as well as the potential capacity of these mesoscale assemblies to remodel chromatin in response to diverse stressors at different length and time scales.
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Affiliation(s)
| | | | - Tumara Boyd
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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5
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Yu S, Zhao J, Chu R, Li X, Wu G, Meng X. Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25050796. [PMID: 37238551 DOI: 10.3390/e25050796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
This work provides mesoscale models for the anomalous diffusion of a polymer chain on a heterogeneous surface with rearranging randomly distributed adsorption sites. Both the "bead-spring" model and oxDNA model were simulated on supported lipid bilayer membranes with various molar fractions of charged lipids, using Brownian dynamics method. Our simulation results demonstrate that "bead-spring" chains exhibit sub-diffusion on charged lipid bilayers which agrees with previous experimental observations for short-time dynamics of DNA segments on membranes. In addition, the non-Gaussian diffusive behaviors of DNA segments have not been observed in our simulations. However, a simulated 17 base pairs double stranded DNA, using oxDNA model, performs normal diffusion on supported cationic lipid bilayers. Due to the number of positively charged lipids attracted by short DNA is small, the energy landscape that the short DNA experiences during diffusion is not as heterogeneous as that experienced by long DNA chains, which results in normal diffusion rather than sub-diffusion for short DNA.
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Affiliation(s)
- Shi Yu
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
| | - Jianqiao Zhao
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
| | - Ruizhi Chu
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
- Key Laboratory of Coal-Based CO2 Capture and Geological Storage, China University of Mining & Technology, Xuzhou 221116, China
| | - Xiao Li
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
- Key Laboratory of Coal-Based CO2 Capture and Geological Storage, China University of Mining & Technology, Xuzhou 221116, China
| | - Guoguang Wu
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
- Key Laboratory of Coal-Based CO2 Capture and Geological Storage, China University of Mining & Technology, Xuzhou 221116, China
| | - Xianliang Meng
- Department of Chemical Engineering, China University of Mining & Technology, Xuzhou 221116, China
- Key Laboratory of Coal-Based CO2 Capture and Geological Storage, China University of Mining & Technology, Xuzhou 221116, China
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6
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Semenov A, Nyrkova I. Adsorption of Wormlike Chains onto Partially Permeable Membranes. Polymers (Basel) 2022; 15:polym15010035. [PMID: 36616385 PMCID: PMC9823683 DOI: 10.3390/polym15010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022] Open
Abstract
Reversible adsorption of a single stiff wormlike macromolecule to flat membranes with various permeabilities is considered theoretically. It is shown that the adsorbed layer microstructure is significantly different from either a flexible chain or a stiff chain adsorption at a solid surface. Close to the critical point, the adsorbing wormlike chain forms a strongly anisotropic proximal layer near the membrane in addition to a nearly isotropic distal layer. The proximal layer is characterized by the algebraic monomer concentration profile, c(x)∝x-β, due to the self-similar distribution of aligned polymer loops. For a perfectly penetrable membrane, β=1 which is different from β=4/3 obtained for semiflexible chain adsorption at a solid surface. Moreover, we establish that the critical exponent for a partially permeable membrane depends on its properties (porosity w) and propose an asymptotically exact theory (based on the generalized Edwards equation) predicting this dependence, β=β(w). We also develop a scaling theory elucidating, in particular, an intricate competition of loops and tails in both proximal and distal sublayers.
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7
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Sachdev S, Potočnik T, Rems L, Miklavčič D. Revisiting the role of pulsed electric fields in overcoming the barriers to in vivo gene electrotransfer. Bioelectrochemistry 2022; 144:107994. [PMID: 34930678 DOI: 10.1016/j.bioelechem.2021.107994] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 12/21/2022]
Abstract
Gene therapies are revolutionizing medicine by providing a way to cure hitherto incurable diseases. The scientific and technological advances have enabled the first gene therapies to become clinically approved. In addition, with the ongoing COVID-19 pandemic, we are witnessing record speeds in the development and distribution of gene-based vaccines. For gene therapy to take effect, the therapeutic nucleic acids (RNA or DNA) need to overcome several barriers before they can execute their function of producing a protein or silencing a defective or overexpressing gene. This includes the barriers of the interstitium, the cell membrane, the cytoplasmic barriers and (in case of DNA) the nuclear envelope. Gene electrotransfer (GET), i.e., transfection by means of pulsed electric fields, is a non-viral technique that can overcome these barriers in a safe and effective manner. GET has reached the clinical stage of investigations where it is currently being evaluated for its therapeutic benefits across a wide variety of indications. In this review, we formalize our current understanding of GET from a biophysical perspective and critically discuss the mechanisms by which electric field can aid in overcoming the barriers. We also identify the gaps in knowledge that are hindering optimization of GET in vivo.
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Affiliation(s)
- Shaurya Sachdev
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Tjaša Potočnik
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Lea Rems
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Damijan Miklavčič
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia.
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8
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Faizi HA, Dimova R, Vlahovska PM. A vesicle microrheometer for high-throughput viscosity measurements of lipid and polymer membranes. Biophys J 2022; 121:910-918. [PMID: 35176271 PMCID: PMC8943812 DOI: 10.1016/j.bpj.2022.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/08/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022] Open
Abstract
Viscosity is a key property of cell membranes that controls mobility of embedded proteins and membrane remodeling. Measuring it is challenging because existing approaches involve complex experimental designs and/or models, and the applicability of some methods is limited to specific systems and membrane compositions. As a result there is scarcity of systematic data, and the reported values for membrane viscosity vary by orders of magnitude for the same system. Here, we show how viscosity of membranes can be easily obtained from the transient deformation of giant unilamellar vesicles. The approach enables a noninvasive, probe-independent, and high-throughput measurement of the viscosity of membranes made of lipids or polymers with a wide range of compositions and phase state. Using this novel method, we have collected a significant amount of data that provides insights into the relation between membrane viscosity, composition, and structure.
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Affiliation(s)
- Hammad A Faizi
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, Potsdam, Germany
| | - Petia M Vlahovska
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois.
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9
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Jahl PE, Parthasarathy R. Assessing the use of ellipsoidal microparticles for determining lipid membrane viscosity. Biophys J 2021; 120:5513-5520. [PMID: 34800470 PMCID: PMC8715235 DOI: 10.1016/j.bpj.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
The viscosity of lipid membranes sets the timescales of membrane-associated motions, whether driven or diffusive, and therefore influences the dynamics of a wide range of cellular processes. Techniques to measure membrane viscosity remain sparse, however, and reported measurements to date, even of similar systems, give viscosity values that span orders of magnitude. To address this, we improve a method based on measuring both the rotational and translational diffusion of membrane-anchored microparticles and apply this approach and one based on tracking the motion of phase-separated lipid domains to the same system of phase-separated giant vesicles. We find good agreement between the two methods, with inferred viscosities within a factor of two of each other. Our single-particle tracking technique uses ellipsoidal microparticles, and we show that the extraction of physically meaningful viscosity values from their motion requires consideration of their anisotropic shape. The validation of our method on phase-separated membranes makes possible its application to other systems, which we demonstrate by measuring the viscosity of bilayers composed of lipids with different chain lengths ranging from 14 to 20 carbon atoms, revealing a very weak dependence of two-dimensional viscosity on lipid size. The experimental and analysis methods described here should be generally applicable to a variety of membrane systems, both reconstituted and cellular.
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Affiliation(s)
- Philip E Jahl
- Materials Science Institute and Department of Physics, The University of Oregon, Eugene, OR, USA
| | - Raghuveer Parthasarathy
- Materials Science Institute and Department of Physics, The University of Oregon, Eugene, OR, USA.
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10
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Lamura A, Winkler RG, Gompper G. Wall-anchored semiflexible polymer under large amplitude oscillatory shear flow. J Chem Phys 2021; 154:224901. [PMID: 34241216 DOI: 10.1063/5.0051427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The properties of semiflexible polymers tethered by one end to an impenetrable wall and exposed to oscillatory shear flow are investigated by mesoscale simulations. A polymer, confined in two dimensions, is described by a linear bead-spring chain, and fluid interactions are incorporated by the Brownian multiparticle collision dynamics approach. At small strain, the polymers follow the applied flow field. However, at high strain, we find a strongly nonlinear response with major conformational changes. Polymers are stretched along the flow direction and exhibit U-shaped conformations while following the flow. As a consequence of confinement in the half-space, frequency doubling in the time-dependent polymer properties appears along the direction normal to the wall.
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Affiliation(s)
- Antonio Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126 Bari, Italy
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute for Advanced Simulation and Institute of Biological Information Processing, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute for Advanced Simulation and Institute of Biological Information Processing, Forschungszentrum Jülich, 52425 Jülich, Germany
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11
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Amador GJ, van Dijk D, Kieffer R, Aubin-Tam ME, Tam D. Hydrodynamic shear dissipation and transmission in lipid bilayers. Proc Natl Acad Sci U S A 2021; 118:e2100156118. [PMID: 34021088 PMCID: PMC8166104 DOI: 10.1073/pnas.2100156118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vital biological processes, such as trafficking, sensing, and motility, are facilitated by cellular lipid membranes, which interact mechanically with surrounding fluids. Such lipid membranes are only a few nanometers thick and composed of a liquid crystalline structure known as the lipid bilayer. Here, we introduce an active, noncontact, two-point microrheology technique combining multiple optical tweezers probes with planar freestanding lipid bilayers accessible on both sides. We use the method to quantify both fluid slip close to the bilayer surface and transmission of fluid flow across the structure, and we use numerical simulations to determine the monolayer viscosity and the intermonolayer friction. We find that these physical properties are highly dependent on the molecular structure of the lipids in the bilayer. We compare ordered-phase with liquid disordered-phase lipid bilayers, and we find the ordered-phase bilayers to be 10 to 100 times more viscous but with 100 times less intermonolayer friction. When a local shear is applied by the optical tweezers, the ultralow intermonolayer friction results in full slip of the two leaflets relative to each other and as a consequence, no shear transmission across the membrane. Our study sheds light on the physical principles governing the transfer of shear forces by and through lipid membranes, which underpin cell behavior and homeostasis.
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Affiliation(s)
- Guillermo J Amador
- Laboratory for Aero and Hydrodynamics, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Delft 2628 CD, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
- Experimental Zoology Group, Wageningen University & Research, Wageningen 6708 WD, The Netherlands
| | - Dennis van Dijk
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Roland Kieffer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands;
| | - Daniel Tam
- Laboratory for Aero and Hydrodynamics, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Delft 2628 CD, The Netherlands;
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12
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Zuraw-Weston SE, Siavashpouri M, Moustaka ME, Gerling T, Dietz H, Fraden S, Ribbe AE, Dinsmore AD. Membrane Remodeling by DNA Origami Nanorods: Experiments Exploring the Parameter Space for Vesicle Remodeling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6219-6231. [PMID: 33983740 DOI: 10.1021/acs.langmuir.1c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Inspired by the ability of cell membranes to alter their shape in response to bound particles, we report an experimental study of long, slender nanorods binding to lipid bilayer vesicles and altering the membrane shape. Our work illuminates the role of particle concentration, adhesion strength, and membrane tension in determining the membrane morphology. We combined giant unilamellar vesicles with oppositely charged nanorods, carefully tuning the adhesion strength, membrane tension, and particle concentration. With increasing adhesion strength, the primary behaviors observed were membrane deformation, vesicle-vesicle adhesion, and vesicle rupture. These behaviors were observed in well-defined regions in the parameter space with sharp transitions between them. We observed the deformation of the membrane resulting in tubulation, textured surfaces, and small and large lipid-particle aggregates. These responses are robust and repeatable and provide a new physical understanding of the dependence on the shape, binding affinity, and particle concentration in membrane remodeling. The design principles derived from these experiments may lead to new bioinspired membrane-based materials.
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Affiliation(s)
- Sarah E Zuraw-Weston
- Department of Physics, University of Massachusetts Amherst, Hasbrouck Lab, 666 North Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Mahsa Siavashpouri
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Maria E Moustaka
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Thomas Gerling
- Department of Physics, Technical University of Munich, James-Franck-Str., 1, Garching D-85748, Germany
| | - Hendrik Dietz
- Department of Physics, Technical University of Munich, James-Franck-Str., 1, Garching D-85748, Germany
| | - Seth Fraden
- Department of Physics, Brandeis University, Abelson-Bass-Yalem, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Alexander E Ribbe
- Department of Polymer Science and Engineering, Silvio O. Conte National Center for Polymer Research, University of Massachusetts Amherst, 120 Governors Drive, Amherst, Massachusetts 01003, United States
| | - Anthony D Dinsmore
- Department of Physics, University of Massachusetts Amherst, Hasbrouck Lab, 666 North Pleasant Street, Amherst, Massachusetts 01002, United States
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13
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Sakuma Y, Kawakatsu T, Taniguchi T, Imai M. Viscosity Landscape of Phase-Separated Lipid Membrane Estimated from Fluid Velocity Field. Biophys J 2020; 118:1576-1587. [PMID: 32053773 PMCID: PMC7136286 DOI: 10.1016/j.bpj.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/24/2019] [Accepted: 01/13/2020] [Indexed: 01/08/2023] Open
Abstract
In cell membranes, the functional constituents such as peptides, proteins, and polysaccharides diffuse in a sea of lipids as single molecules and molecular aggregates. Thus, the fluidity of the heterogeneous multicomponent membrane is important for understanding the roles of the membrane in cell functionality. Recently, Henle and Levine described the hydrodynamics of molecular diffusion in a spherical membrane. A tangential point force at the north pole induces a pair of vortices whose centers lie on a line perpendicular to the point force and are symmetrical with respect to the point force. The position of the vortex center depends on ηm/Rηw, where R is the radius of the spherical membrane, and ηm and ηw are the viscosities of the membrane and the surrounding medium, respectively. Based on this theoretical prediction, we applied a point force to a phase-separated spherical vesicle composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phosphocholine/cholesterol by means of a microinjection technique. The pathlines were visualized by trajectories of microdomains. We determined the position of the vortex center and estimated the membrane viscosity using the dependence of the position of the vortex center on ηm/Rηw. The obtained apparent membrane viscosities for various compositions are mapped on the phase diagram. The membrane viscosity is almost constant in the range of 0 <ϕLo ≤ 0.5 (ϕLo: area fraction of the liquid ordered phase), whereas that in the range of 0.5 ≤ ϕLo < 1.0 exponentially increases with increase of ϕLo. The obtained viscosity landscape provides a basic understanding of the fluidity of heterogeneous multicomponent membranes.
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Affiliation(s)
- Yuka Sakuma
- Department of Physics, Tohoku University, Sendai, Japan.
| | | | | | - Masayuki Imai
- Department of Physics, Tohoku University, Sendai, Japan
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14
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Chwastek G, Petrov EP, Sáenz JP. A Method for High-Throughput Measurements of Viscosity in Sub-micrometer-Sized Membrane Systems. Chembiochem 2020; 21:836-844. [PMID: 31566864 PMCID: PMC7154536 DOI: 10.1002/cbic.201900510] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/27/2019] [Indexed: 01/11/2023]
Abstract
To unravel the underlying principles of membrane adaptation in small systems like bacterial cells, robust approaches to characterize membrane fluidity are needed. Currently available relevant methods require advanced instrumentation and are not suitable for high-throughput settings needed to elucidate the biochemical pathways involved in adaptation. We developed a fast, robust, and financially accessible quantitative method to measure the microviscosity of lipid membranes in bulk suspension using a commercially available plate reader. Our approach, which is suitable for high-throughput screening, is based on the simultaneous measurements of absorbance and fluorescence emission of a viscosity-sensitive fluorescent dye, 9-(2,2-dicyanovinyl)julolidine (DCVJ), incorporated into a lipid membrane. We validated our method using artificial membranes with various lipid compositions over a range of temperatures and observed values that were in good agreement with previously published results. Using our approach, we were able to detect a lipid phase transition in the ruminant pathogen Mycoplasma mycoides.
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Affiliation(s)
- Grzegorz Chwastek
- B CUBE, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Eugene P Petrov
- Faculty of Physics, Ludwig Maximilian University of Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - James Peter Sáenz
- B CUBE, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
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15
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Sachdev S, Feijoo Moreira S, Keehnen Y, Rems L, Kreutzer MT, Boukany PE. DNA-membrane complex formation during electroporation is DNA size-dependent. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183089. [DOI: 10.1016/j.bbamem.2019.183089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 09/11/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023]
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16
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Khmelinskaia A, Mücksch J, Petrov EP, Franquelim HG, Schwille P. Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14921-14931. [PMID: 30253101 DOI: 10.1021/acs.langmuir.8b01850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA origami nanotechnology is being increasingly used to mimic membrane-associated biophysical phenomena. Although a variety of DNA origami nanostructures has already been produced to target lipid membranes, the requirements for membrane binding have so far not been systematically assessed. Here, we used a set of elongated DNA origami structures with varying placement and number of cholesteryl-based membrane anchors to compare different strategies for their incorporation. Single and multiple cholesteryl anchors were attached to DNA nanostructures using single- and double-stranded DNA spacers of varying length. The produced DNA nanostructures were studied in terms of their membrane binding and diffusion. Our results show that the location and number of anchoring moieties play a crucial role for membrane binding of DNA nanostructures mainly if the cholesteryl anchors are in close proximity to the bulky DNA nanostructures. Moreover, the use of DNA spacers largely overcomes local steric hindrances and thus enhances membrane binding. Fluorescence correlation spectroscopy measurements demonstrate that the distinct physical properties of single- and double-stranded DNA spacers control the interaction of the amphipathic DNA nanostructures with lipid membranes. Thus, we provide a rational basis for the design of amphipathic DNA origami nanostructures to efficiently bind lipid membranes in various environments.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Eugene P Petrov
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
- Faculty of Physics , Ludwig Maximilian University of Munich , Geschwister-Scholl-Platz 1 , 80539 Munich , Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
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17
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Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context. Biointerphases 2018; 13:028501. [DOI: 10.1116/1.5022145] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Khmelinskaia A, Mücksch J, Conci F, Chwastek G, Schwille P. FCS Analysis of Protein Mobility on Lipid Monolayers. Biophys J 2018; 114:2444-2454. [PMID: 29605081 DOI: 10.1016/j.bpj.2018.02.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/08/2018] [Accepted: 02/27/2018] [Indexed: 02/01/2023] Open
Abstract
In vitro membrane model systems are used to dissect complex biological phenomena under controlled unadulterated conditions. In this context, lipid monolayers are a powerful tool to particularly study the influence of lipid packing on the behavior of membrane proteins. Here, monolayers deposited in miniaturized fixed area-chambers, which require only minute amounts of protein, were used and shown to faithfully reproduce the characteristics of Langmuir monolayers. This assay is ideally suited to be combined with single-molecule sensitive fluorescence correlation spectroscopy (FCS) to characterize diffusion dynamics. Our results confirm the influence of lipid packing on lipid mobility and validate the use of FCS as an alternative to conventional surface pressure measurements for characterizing the monolayer. Furthermore, we demonstrate the effect of lipid density on the diffusional behavior of membrane-bound components. We exploit the sensitivity of FCS to characterize protein interactions with the lipid monolayer in a regime in which the monolayer physical properties are not altered. To demonstrate the potential of our approach, we analyzed the diffusion behavior of objects of different nature, ranging from a small peptide to a large DNA-based nanostructure. Moreover, in this work we quantify the surface viscosity of lipid monolayers. We present a detailed strategy for the conduction of point FCS experiments on lipid monolayers, which is the first step toward extensive studies of protein-monolayer interactions.
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Affiliation(s)
- Alena Khmelinskaia
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonas Mücksch
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Franco Conci
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Grzegorz Chwastek
- 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.
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19
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Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS NANO 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
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Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
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20
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Chelladurai R, Debnath K, Jana NR, Basu JK. Nanoscale Heterogeneities Drive Enhanced Binding and Anomalous Diffusion of Nanoparticles in Model Biomembranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1691-1699. [PMID: 29320202 DOI: 10.1021/acs.langmuir.7b04003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Interaction of functional nanoparticles with cells and model biomembranes has been widely studied to evaluate the effectiveness of the particles as potential drug delivery vehicles and bioimaging labels as well as in understanding nanoparticle cytotoxicity effects. Charged nanoparticles, in particular, with tunable surface charge have been found to be effective in targeting cellular membranes as well as the subcellular matrix. However, a microscopic understanding of the underlying physical principles that govern nanoparticle binding, uptake, or diffusion on cells is lacking. Here, we report the first experimental studies of nanoparticle diffusion on model biomembranes and correlate this to the existence of nanoscale dynamics and structural heterogeneities using super-resolution stimulated emission depletion (STED) microscopy. Using confocal and STED microscopy coupled with fluorescence correlation spectroscopy (FCS), we provide novel insight on why these nanoparticles show enhanced binding on two-component lipid bilayers as compared to single-component membranes and how binding and diffusion is correlated to subdiffraction nanoscale dynamics and structure. The enhanced binding is also dictated, in part, by the presence of structural and dynamic heterogeneity, as revealed by STED-FCS studies, which could potentially be used to understand enhanced nanoparticle binding in raft-like domains in cell membranes. In addition, we also observe a clear correlation between the enhanced nanoparticle diffusion on membranes and the extent of membrane penetration by the nanoparticles. Our results not only have a significant impact on our understanding of nanoparticle binding and uptake as well as diffusion in cell and biomembranes, but have very strong implications for uptake mechanisms and diffusion of other biomolecules, like proteins on cell membranes and their connections to functional membrane nanoscale platform.
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Affiliation(s)
- Roobala Chelladurai
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
| | - Koushik Debnath
- Centre for Advanced Materials, Indian Association for the Cultivation of Sciences , Kolkata 700032, India
| | - Nikhil R Jana
- Centre for Advanced Materials, Indian Association for the Cultivation of Sciences , Kolkata 700032, India
| | - Jaydeep Kumar Basu
- Department of Physics, Indian Institute of Science , Bangalore 560012, India
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21
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Li B, Abel SM. Shaping membrane vesicles by adsorption of a semiflexible polymer. SOFT MATTER 2018; 14:185-193. [PMID: 29143046 DOI: 10.1039/c7sm01751k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The adsorption of polymers onto fluid membranes is a problem of fundamental interest in biology and soft materials, in part because the flexibility of membranes can lead to nontrivial coupling between polymer and membrane configurations. Here, we use Monte Carlo computer simulations to study the adsorption of a semiflexible polymer onto a fluid membrane vesicle. Polymer adsorption can significantly impact both the vesicle and polymer shapes, and we identify distinct classes of configurations that emerge as a function of polymer persistence length, membrane bending rigidity, adsorption strength, and vesicle size. Large-scale deformations of the vesicle include invaginations of the membrane that internalize the polymer in a membrane bud. The buds range from disk-like shapes surrounding a collapsed polymer to tubular deformations enveloping rod-like polymers. For small vesicles, polymer adsorption also induces dumbbell-like vesicle shapes with a narrow membrane constriction circled by the polymer. Vesicles with sufficiently small or large bending rigidities adopt configurations similar to those without the polymer present. We further characterize statistical properties of the membrane and polymer configurations and identify distinct classes of polymer configurations that emerge within membrane buds. Analysis of idealized polymer-membrane configurations provides additional insight into transitions between bud shapes.
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Affiliation(s)
- Bing Li
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
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22
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Microparticle Assembly Pathways on Lipid Membranes. Biophys J 2017; 113:1037-1046. [PMID: 28877487 DOI: 10.1016/j.bpj.2017.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 11/20/2022] Open
Abstract
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force between microparticles and model lipid membranes causes membrane-mediated particle assembly. Using confocal microscopy, we observe the initial particle attachment to the membrane, then particle wrapping, and in rare cases spontaneous membrane tubulation. In the attached state, we measure that the particle mobility decreases by 26%. If multiple particles adhere to the same vesicle, their initial single-particle state determines their interactions and subsequent assembly pathways: 1) attached particles only aggregate when small adhesive vesicles are present in solution, 2) wrapped particles reversibly attract one another by membrane deformation, and 3) a combination of wrapped and attached particles form membrane-mediated dimers, which further assemble into a variety of complex structures. The experimental observation of distinct assembly pathways, induced only by a short-ranged membrane-particle adhesion, shows that a cytoskeleton or other active components are not required for microparticle aggregation. We suggest that this membrane-mediated microparticle aggregation is a reason behind reported long retention times of polymer microparticles in organisms.
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23
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Petrova AB, Herold C, Petrov EP. Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes. SOFT MATTER 2017; 13:7172-7187. [PMID: 28930355 DOI: 10.1039/c7sm00829e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 μm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.
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Affiliation(s)
- Anastasiia B Petrova
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, 82152 Martinsried, Germany.
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24
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Joniova J, Rebič M, Strejčková A, Huntosova V, Staničová J, Jancura D, Miskovsky P, Bánó G. Formation of Large Hypericin Aggregates in Giant Unilamellar Vesicles-Experiments and Modeling. Biophys J 2017; 112:966-975. [PMID: 28297655 DOI: 10.1016/j.bpj.2017.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/16/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
The incorporation of hypericin (Hyp) from aqueous solutions into giant unilamellar vesicle (GUV) membranes has been studied experimentally and by means of kinetic Monte Carlo modeling. The time evolution of Hyp fluorescence originating from Hyp monomers dissolved in the GUV membrane has been recorded by confocal microscopy and while trapping individual GUVs in optical tweezers. It was shown that after reaching a maximum, the fluorescence intensity gradually decreased toward longer times. Formation of oversized Hyp clusters has been observed on the GUV surface at prolonged time. A simplified kinetic Monte Carlo model is presented to follow the aggregation/dissociation processes of Hyp molecules in the membrane. The simulation results reproduced the basic experimental observations: the scaling of the characteristic fluorescence decay time with the vesicle diameter and the buildup of large Hyp clusters in the GUV membrane.
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Affiliation(s)
- Jaroslava Joniova
- Department of Biophysics, Institute of Physics, Faculty of Science, P.J. Šafárik University, Košice, Slovakia; Laboratory of Organometallic and Medicinal Chemistry, ISIC, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Matúš Rebič
- Department of Biophysics, Institute of Physics, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
| | - Alena Strejčková
- Department of Chemistry, Biochemistry and Biophysics, Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Veronika Huntosova
- Center for Interdisciplinary Biosciences, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
| | - Jana Staničová
- Department of Chemistry, Biochemistry and Biophysics, Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Daniel Jancura
- Department of Biophysics, Institute of Physics, Faculty of Science, P.J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
| | - Pavol Miskovsky
- Department of Biophysics, Institute of Physics, Faculty of Science, P.J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
| | - Gregor Bánó
- Department of Biophysics, Institute of Physics, Faculty of Science, P.J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Science, P.J. Šafárik University, Košice, Slovakia.
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25
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Cai Y, Shashikanth N, Leckband DE, Schwartz DK. Cadherin Diffusion in Supported Lipid Bilayers Exhibits Calcium-Dependent Dynamic Heterogeneity. Biophys J 2017; 111:2658-2665. [PMID: 28002742 DOI: 10.1016/j.bpj.2016.10.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/14/2016] [Accepted: 10/31/2016] [Indexed: 11/16/2022] Open
Abstract
Ca2+ ions are critical to cadherin ectodomain rigidity, which is required for the activation of adhesive functions. Therefore, changes in Ca2+ concentration, both in vivo and in vitro, can affect cadherin conformation and function. We employed single-molecule tracking to measure the diffusion of cadherin ectodomains tethered to supported lipid bilayers at varying Ca2+ concentrations. At a relatively high Ca2+ concentration of 2 mM, cadherin molecules exhibited a fast diffusion coefficient that was identical to that of individual lipid molecules in the bilayer (Dfast ≈ 3 μm2/s). At lower Ca2+ concentrations, where cadherin molecules were less rigid, the ensemble-average cadherin diffusion coefficient was systematically smaller. Individual cadherin trajectories were temporally heterogeneous, exhibiting alternating periods of fast and slow diffusion; the periods of slow diffusion (Dslow ≈ 0.1 μm2/s) were more prevalent at lower Ca2+ concentration. These observations suggested that more flexible cadherin ectodomains at lower Ca2+ concentration alternated between upright and lying-down conformations, where the latter interacted with more lipid molecules and experienced greater viscous drag.
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Affiliation(s)
- Yu Cai
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Nitesh Shashikanth
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Deborah E Leckband
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.
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26
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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.
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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.
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27
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Chen P, Huang Z, Liang J, Cui T, Zhang X, Miao B, Yan LT. Diffusion and Directionality of Charged Nanoparticles on Lipid Bilayer Membrane. ACS NANO 2016; 10:11541-11547. [PMID: 27936576 DOI: 10.1021/acsnano.6b07563] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Diffusion dynamics of charged nanoparticles on the lipid membrane is of essential importance to cellular functioning. Yet a fundamental insight into electrostatics-mediated diffusion dynamics of charged nanoparticles on the membrane is lacking and remains to be an urgent issue. Here we present the computational investigation to uncover the pivotal role of electrostatics in the diffusion dynamics of charged nanoparticles on the lipid membrane. Our results demonstrate diffusive behaviors and directional transport of a charged nanoparticle, significantly depending on the sign and spatial distribution of charges on its surface. In contrast to the Fickian diffusion of neutral nanoparticles, randomly charged nanoparticles undergo superdiffusive transport with directionality. However, the dynamics of uniformly charged nanoparticles favors Fickian diffusion that is significantly enhanced. Such observations can be explained in term of electrostatics-induced surface reconstruction and fluctuation of lipid membrane. We finally present an analytical model connecting surface reconstruction and local deformation of the membrane. Our findings bear wide implications for the understanding and control of the transport of charged nanoparticles on the cell membrane.
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Affiliation(s)
- Pengyu Chen
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Zihan Huang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Junshi Liang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Tianqi Cui
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Xinghua Zhang
- School of Science, Beijing Jiaotong University , Beijing 100044, China
| | - Bing Miao
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Li-Tang Yan
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
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28
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Ghosh SK, Cherstvy AG, Petrov EP, Metzler R. Interactions of rod-like particles on responsive elastic sheets. SOFT MATTER 2016; 12:7908-19. [PMID: 27492050 DOI: 10.1039/c6sm01522k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? To rationalise this, we here investigate by extensive computer simulations mutual interactions of rod-like particles adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. We demonstrate that tip-to-tip contacts of rods are favoured for relatively soft sheets, while side-by-side contacts are preferred for stiffer elastic substrates. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The optimal orientation of the membrane-bound rods is established via responding to the elastic energy profiles created around the particles. We unveil the phase diagramme of attractive-repulsive rod-rod interactions in the plane of their separation and mutual orientation. Applications of our results to other systems featuring membrane-associated particles are also discussed.
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Affiliation(s)
- Surya K Ghosh
- TIMC-IMAG Laboratory, Universite Grenoble Alpes, CNRS UMR, 5525 Grenoble, France
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Metzler R, Jeon JH, Cherstvy AG. Non-Brownian diffusion in lipid membranes: Experiments and simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2451-2467. [PMID: 26826272 DOI: 10.1016/j.bbamem.2016.01.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 12/14/2022]
Abstract
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane-binding particles. We discuss how membrane compartmentalisation and the particle-membrane binding energy may impact the dynamics and response of lipid membranes. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- R Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany; Department of Physics, Tampere University of Technology, 33101 Tampere, Finland.
| | - J-H Jeon
- Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea
| | - A G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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Camley BA, Brown FLH. Fluctuating hydrodynamics of multicomponent membranes with embedded proteins. J Chem Phys 2015; 141:075103. [PMID: 25149817 DOI: 10.1063/1.4892802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A simulation method for the dynamics of inhomogeneous lipid bilayer membranes is presented. The membrane is treated using stochastic Saffman-Delbrück hydrodynamics, coupled to a phase-field description of lipid composition and discrete membrane proteins. Multiple applications are considered to validate and parameterize the model. The dynamics of membrane composition fluctuations above the critical point and phase separation dynamics below the critical point are studied in some detail, including the effects of adding proteins to the mixture.
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Affiliation(s)
- Brian A Camley
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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Hamada T, Fujimoto R, Shimobayashi SF, Ichikawa M, Takagi M. Molecular behavior of DNA in a cell-sized compartment coated by lipids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062717. [PMID: 26172746 DOI: 10.1103/physreve.91.062717] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Indexed: 06/04/2023]
Abstract
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space. Globular DNA showed a cell-size-dependent unfolding transition after adsorption on the membrane. Furthermore, when DNA interacted with a two-phase membrane surface, DNA selectively adsorbed on the membrane phase, such as an ordered or disordered phase, depending on its conformation. We discuss the mechanism of these trends by considering the free energy of DNA together with a polyamine in the solution. The free energy of our model was consistent with the present experimental data. The cooperative interaction of DNA and polyamines with a membrane surface leads to the size-dependent behavior of molecular systems in a small space. These findings may contribute to a better understanding of the physical mechanism of molecular events and reactions inside a cell.
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Affiliation(s)
- Tsutomu Hamada
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Rie Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | | | - Masatoshi Ichikawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Cherstvy AG, Petrov EP. Modeling DNA condensation on freestanding cationic lipid membranes. Phys Chem Chem Phys 2014; 16:2020-37. [PMID: 24343177 DOI: 10.1039/c3cp53433b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Motivated by recent experimental observations of a rapid spontaneous DNA coil-globule transition on freestanding cationic lipid bilayers, we propose simple theoretical models for DNA condensation on cationic lipid membranes. First, for a single DNA rod, we examine the conditions of full wrapping of a cylindrical DNA-like semi-flexible polyelectrolyte by an oppositely charged membrane. Then, for two parallel DNA rods, we self-consistently analyze the shape and the extent of the membrane enveloping them, focusing on membrane elastic deformations and the membrane-DNA embracing angle, which enables us to compute the membrane-mediated DNA-DNA interactions. We examine the effects of the membrane composition and its charge density, which are the experimentally tunable parameters. We show that membrane-driven rod-rod attraction is more pronounced for higher charge densities and for smaller surface tensions of the membrane. Thus, we demonstrate that for a long DNA chain adhered to a cationic lipid membrane, such membrane-induced DNA-DNA attraction can trigger compaction of DNA.
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Affiliation(s)
- Andrey G Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany.
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Hormel TT, Kurihara SQ, Brennan MK, Wozniak MC, Parthasarathy R. Measuring lipid membrane viscosity using rotational and translational probe diffusion. PHYSICAL REVIEW LETTERS 2014; 112:188101. [PMID: 24856725 DOI: 10.1103/physrevlett.112.188101] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Indexed: 05/23/2023]
Abstract
The two-dimensional fluidity of lipid bilayers enables the motion of membrane-bound macromolecules and is therefore crucial to biological function. Microrheological methods that measure fluid viscosity via the translational diffusion of tracer particles are challenging to apply and interpret for membranes, due to uncertainty about the local environment of the tracers. Here, we demonstrate a new technique in which determination of both the rotational and translational diffusion coefficients of membrane-linked particles enables quantification of viscosity, measurement of the effective radii of the tracers, and assessment of theoretical models of membrane hydrodynamics. Surprisingly, we find a wide distribution of effective tracer radii, presumably due to a variable number of lipids linked to each tracer particle. Furthermore, we show for the first time that a protein involved in generating membrane curvature, the vesicle trafficking protein Sar1p, dramatically increases membrane viscosity. Using the rheological method presented here, therefore, we are able to reveal a class of previously unknown couplings between protein activity and membrane mechanics.
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Affiliation(s)
- Tristan T Hormel
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Sarah Q Kurihara
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - M Kathleen Brennan
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Matthew C Wozniak
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
| | - Raghuveer Parthasarathy
- Department of Physics and Materials Science Institute, University of Oregon, Eugene, Oregon 97401, USA
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Czogalla A, Petrov EP, Kauert DJ, Uzunova V, Zhang Y, Seidel R, Schwille P. Switchable domain partitioning and diffusion of DNA origami rods on membranes. Faraday Discuss 2013; 161:31-43; discussion 113-50. [DOI: 10.1039/c2fd20109g] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Herold C, Chwastek G, Schwille P, Petrov EP. Efficient electroformation of supergiant unilamellar vesicles containing cationic lipids on ITO-coated electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:5518-21. [PMID: 22424289 DOI: 10.1021/la3005807] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Giant unilamellar vesicles (GUVs) represent a versatile in vitro system widely used to study properties of lipid membranes and their interaction with biomacromolecules and colloids. Electroformation with indium tin oxide (ITO) coated coverslips as electrodes is a standard approach to GUV production. In the case of cationic GUVs, however, application of this approach leads to notorious difficulties. We discover that this is related to aging of ITO-coated coverslips during their repeated use, which is reflected in their surface topography on the nanoscale. We find that mild annealing of the ITO-coated surface in air reverts the effects of aging and ensures efficient reproducible electroformation of supergiant (diameter > 100 μm) unilamellar vesicles containing cationic lipids.
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Affiliation(s)
- Christoph Herold
- Biophysics, BIOTEC, Technische Universität Dresden, Dresden, Germany
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Ramachandran S, Komura S, Seki K, Gompper G. Dynamics of a polymer chain confined in a membrane. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:46. [PMID: 21562968 DOI: 10.1140/epje/i2011-11046-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 12/18/2010] [Accepted: 03/30/2011] [Indexed: 05/30/2023]
Abstract
We present a Brownian dynamics theory with full hydrodynamics (Stokesian dynamics) for a Gaussian polymer chain embedded in a liquid membrane which is surrounded by bulk solvent and walls. The mobility tensors are derived in Fourier space for the two geometries, namely, a free membrane embedded in a bulk fluid, and a membrane sandwiched by the two walls. Within the preaveraging approximation, a new expression for the diffusion coefficient of the polymer is obtained for the free-membrane geometry. We also carry out a Rouse normal mode analysis to obtain the relaxation time and the dynamical structure factor. For large polymer size, both quantities show Zimm-like behavior in the free-membrane case, whereas they are Rouse-like for the sandwiched membrane geometry. We use the scaling argument to discuss the effect of excluded-volume interactions on the polymer relaxation time.
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Affiliation(s)
- S Ramachandran
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Japan
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37
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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38
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Nguyen ZH, Atkinson M, Park CS, Maclennan J, Glaser M, Clark N. Crossover between 2D and 3D fluid dynamics in the diffusion of islands in ultrathin freely suspended smectic films. PHYSICAL REVIEW LETTERS 2010; 105:268304. [PMID: 21231720 DOI: 10.1103/physrevlett.105.268304] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Indexed: 05/30/2023]
Abstract
The Stokes paradox, that moving a disk at finite velocity through an infinite two-dimensional (2D) viscous fluid requires no force, leads, via the Einstein relation, to an infinite diffusion coefficient D for the disk. Saffman and Delbrück proposed that if the 2D fluid is a thin film immersed in a 3D viscous medium, then the film should behave as if it were of finite size, and D∼ -ln(aη'), where a is the inclusion radius and η' is the viscosity of the 3D medium. By studying the Brownian motion of islands in freely suspended smectic liquid crystal films a few molecular layers thick, we verify this dependence using no free parameters, and confirm the subsequent prediction by Hughes, Pailthorpe, and White of a crossover to 3D Stokes-like behavior when the diffusing island is sufficiently large.
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Affiliation(s)
- Zoom Hoang Nguyen
- Department of Physics and LCMRC, University of Colorado, Boulder, Colorado, USA
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Spruijt E, Sprakel J, Lemmers M, Stuart MAC, van der Gucht J. Relaxation dynamics at different time scales in electrostatic complexes: time-salt superposition. PHYSICAL REVIEW LETTERS 2010; 105:208301. [PMID: 21231268 DOI: 10.1103/physrevlett.105.208301] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Indexed: 05/03/2023]
Abstract
In this Letter we show that in the rheology of electrostatically assembled soft materials, salt concentration plays a similar role as temperature for polymer melts, and as strain rate for soft solids. We rescale linear and nonlinear rheological data of a set of model electrostatic complexes at different salt concentrations to access a range of time scales that is otherwise inaccessible. This provides new insights into the relaxation mechanisms of electrostatic complexes, which we rationalize in terms of a microscopic mechanism underlying salt-enhanced activated processes.
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.
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Garcia-Manyes S, Redondo-Morata L, Oncins G, Sanz F. Nanomechanics of Lipid Bilayers: Heads or Tails? J Am Chem Soc 2010; 132:12874-86. [DOI: 10.1021/ja1002185] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sergi Garcia-Manyes
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Lorena Redondo-Morata
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Gerard Oncins
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
| | - Fausto Sanz
- Department of Biological Sciences, Columbia University, New York, 10027, New York, Departament de Química Física, Universitat de Barcelona, 08028, Spain, Institut de Bioenginyeria de Catalunya, Barcelona, 08028, Spain, Serveis Cientificotècnics, Universitat de Barcelona, 08028, Spain, and CIBER-BBN, Zaragoza 50018, Spain
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