1
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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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2
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Budkov YA, Brandyshev PE, Kalikin NN. Theory of self-coacervation in semi-dilute and concentrated zwitterionic polymer solutions. SOFT MATTER 2023; 19:3281-3289. [PMID: 37089119 DOI: 10.1039/d3sm00140g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Based on the random phase approximation, we develop a molecular theory of self-coacervation in zwitterionic polymer solutions. We show that the interplay between the volume interactions of the monomeric units and electrostatic correlations of charged groups on a polymer backbone can result in liquid-liquid phase separation (self-coacervation). We analyse the behavior of the coacervate phase polymer concentration depending on the electrostatic interaction strength - the ratio of the Bjerrum length to the bond length of the chain. We establish that in a wide range of polymer concentration values - from a semi-dilute to a rather concentrated solution - the chain connectivity and excluded volume interaction of the monomeric units have an extremely weak effect on the contribution of the electrostatic interactions of the dipolar monomeric units to the total free energy. We show that for rather weak electrostatic interactions, the electrostatic correlations manifest themselves as Keesom interactions of point-like freely rotating dipoles (Keesom regime), while in the region of strong electrostatic interactions the electrostatic free energy is described by the Debye-Hückel limiting law (Debye regime). We show that for real zwitterionic coacervates the Keesom regime is realized only for sufficiently small polymer concentrations of the coacervate phase, while the Debye regime is approximately realized for rather dense coacervates. Using the mean-field variant of the density functional theory, we calculate the surface tension (surface free energy) of the "coacervate-solvent" interface as a function of the bulk polymer concentration. Obtained results can be used to estimate the parameters of the polymer chains needed for practical applications such as drug encapsulation and delivery, as well as the design of adhesive materials.
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Affiliation(s)
- Yury A Budkov
- School of Applied Mathematics, HSE University, Tallinskaya st. 34, 123458 Moscow, Russia.
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo, 153045, Russia
| | - Petr E Brandyshev
- School of Applied Mathematics, HSE University, Tallinskaya st. 34, 123458 Moscow, Russia.
| | - Nikolai N Kalikin
- School of Applied Mathematics, HSE University, Tallinskaya st. 34, 123458 Moscow, Russia.
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo, 153045, Russia
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3
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Quinn SD, Dresser L, Graham S, Conteduca D, Shepherd J, Leake MC. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET. Front Bioeng Biotechnol 2022; 10:958026. [PMID: 36394015 PMCID: PMC9650091 DOI: 10.3389/fbioe.2022.958026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid–protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
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Affiliation(s)
- Steven D. Quinn
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
| | - Lara Dresser
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Sarah Graham
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Donato Conteduca
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
| | - Jack Shepherd
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Mark C. Leake
- School of Physics, Engineering and Technology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- *Correspondence: Mark C. Leake,
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4
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Rapid In-Process Measurement of Live Virus Vaccine Potency Using Laser Force Cytology: Paving the Way for Rapid Vaccine Development. Vaccines (Basel) 2022; 10:vaccines10101589. [PMID: 36298454 PMCID: PMC9608199 DOI: 10.3390/vaccines10101589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Vaccinations to prevent infectious diseases are given to target the body’s innate and adaptive immune systems. In most cases, the potency of a live virus vaccine (LVV) is the most critical measurement of efficacy, though in some cases the quantity of surface antigen on the virus is an equally critical quality attribute. Existing methods to measure the potency of viruses include plaque and TCID50 assays, both of which have very long lead times and cannot provide real time information on the quality of the vaccine during large-scale manufacturing. Here, we report the evaluation of LumaCyte’s Radiance Laser Force Cytology platform as a new way to measure the potency of LVVs in upstream biomanufacturing process in real time and compare this to traditional TCID50 potency. We also assess this new platform as a way to detect adventitious agents, which is a regulatory expectation for the release of commercial vaccines. In both applications, we report the ability to obtain expedited and relevant potency information with strong correlation to release potency methods. Together, our data propose the application of Laser Force Cytology as a valuable process analytical technology (PAT) for the timely measurement of critical quality attributes of LVVs.
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5
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Sarkar MK, Karal MAS, Levadny V, Belaya M, Ahmed M, Ahamed MK, Ahammed S. Effects of sugar concentration on the electroporation, size distribution and average size of charged giant unilamellar vesicles. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:401-412. [PMID: 35716178 DOI: 10.1007/s00249-022-01607-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
We investigated the effects of sugar concentration on the electroporation, size distribution and average size of giant unilamellar vesicles (GUVs). GUVs were prepared from 40 mol% of 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DOPG) and 60 mol% of 1, 2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipids. Pulsed electric field was applied to the 40%DOPG/60%DOPC-GUVs and it induced lateral electric tension (σc) in the membranes of vesicles. The σc-induced probability of rupture (Ppore) and the rate constant of rupture (kp) of GUVs under the sugar concentration, c = 40, 100 and 300 mM, were determined. Both the Ppore and kp increased with the increase of σc, but higher tension was required to generate the same values of Ppore and kp with increasing c. We also investigated average sizes of GUVs from the size distribution of vesicles under various sugar concentrations. With the increase of c, the peak of the size distribution histograms shifted to the region of smaller vesicles. The average size decreased 1.6-fold when c increased from 10 to 300 mM. These investigations help to understand various biomedical, biophysical, and biochemical processes in vesicles and cells. Electroporation, size distribution and average size of charged GUVs were investigated under various sugar concentrations. The sugar concentration influences the electroporation of vesicles and the average size of GUVs.
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Affiliation(s)
- Malay Kumar Sarkar
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
- Department of Arts and Sciences, Ahsanullah University of Science and Technology, Dhaka, 1208, Bangladesh
| | - Mohammad Abu Sayem Karal
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh.
| | - Victor Levadny
- Theoretical Problem Center of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, 117977, Russia
| | - Marina Belaya
- Department of Mathematics, Russian State University for the Humanities, GSP-3, Moscow, 125993, Russia
| | - Marzuk Ahmed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Md Kabir Ahamed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Shareef Ahammed
- Department of Physics, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
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6
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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: 15] [Impact Index Per Article: 7.5] [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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7
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Si DQ, Liu XY, Wu JB, Hu GH. Modulation of DNA conformation in electrolytic nanodroplets. Phys Chem Chem Phys 2022; 24:6002-6010. [PMID: 35199810 DOI: 10.1039/d1cp05329a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.
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Affiliation(s)
- Dong-Qing Si
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Xin-Yue Liu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Jin-Bo Wu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Guo-Hui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
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8
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Klett K, Cherstvy AG, Shin J, Sokolov IM, Metzler R. Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions. Phys Rev E 2022; 104:064603. [PMID: 35030844 DOI: 10.1103/physreve.104.064603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/18/2021] [Indexed: 12/22/2022]
Abstract
We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-of-mass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We study the intradumbbell dynamics of the relative motion of the two constituent elastically coupled disks. Our main focus is on effects of the crowding fraction ϕ and of the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF), and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on ϕ, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from viscous to viscoelastic diffusion upon growing ϕ. We also analyze the relative motion in the dimers, finding that larger ϕ suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(ϕ) of translational and rotational motion of the dumbbells an exponential decay with ϕ for weak and a power-law variation D(ϕ)∝(ϕ-ϕ^{★})^{2.4} for strong crowding is found. A comparison of simulation results with theoretical predictions for D(ϕ) is discussed and some relevant experimental systems are overviewed.
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Affiliation(s)
- Kolja Klett
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G Cherstvy
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.,Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Igor M Sokolov
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany.,IRIS Adlershof, Zum Großen Windkanal 6, 12489 Berlin, Germany
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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9
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Pawłowski PH. Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. Infect Drug Resist 2021; 14:5099-5105. [PMID: 34880635 PMCID: PMC8647725 DOI: 10.2147/idr.s342068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
The change in the formal charge of 34 SARS-CoV-2 lineages from September 2020 to June 2021 was analyzed according to the monthly evidence of the European agency. The reported point mutations and small insertions are electrically neutral (17), positive (12), or negative (3). They had been found in the spike glycoprotein S, in the RBD and S1/S2 regions, crucial for initiation of viral infection. The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively. They are related to G and A switching. Positive mutations are stretching equally in both areas, but in the RBD region, they are more dispersed. In the set of analyzed virus variants, the increasing tendency in the number of positively charged residues in spike protein was observed. Furthermore, the well-documented WHO classes show an increase in the COVID-19 percentage case fatality with the positive increase in the spike crucial region’s total charge. The data mining, applying classifier algorithm based on the artificial neuronal network, confirms that the value and the distribution of additional positive charge in S may be important factors enabling virus impact to immunity. This may be promoted by the stronger long-range electrostatic attraction of the virus particle to the host cell, preceding the infection. The estimation of the potential energy for the RBD approaching the angiotensin-converting enzyme (ACE2) was presented.
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Affiliation(s)
- Piotr H Pawłowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
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10
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Ikeda Y, Nakamura H, Ohsaki S, Watano S. Direct translocation of a negatively charged nanoparticle across a negatively charged model cell membrane. Phys Chem Chem Phys 2021; 23:10591-10599. [PMID: 33903858 DOI: 10.1039/d0cp06278b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanoparticles have attracted much attention as a carrier for drug, gene, and macromolecule delivery in next-generation biomedical and therapeutic technologies. In delivery applications, nanoparticles tend to have negative charge due to the negative charge of biomolecules used as delivery cargo, while biological cell membranes are also negatively charged. This means that negatively charged nanoparticles (NC-NPs) are required to translocate across these negatively charged cell membranes (NC-CMs). However, this translocation is unlikely to occur because of electrostatic interactions. Here, we investigated the translocation of a NC-NP across a NC-CM under a transmembrane electric potential through coarse-grained molecular dynamics simulations. To model the transmembrane potential, two approaches were adopted: externally applied electric field and ionic charge imbalance. We showed that a NC-NP can directly translocate across a NC-CM via a non-disruptive pathway under a weak external electric field with an ionic charge imbalance. It was also found that the ionic charge imbalance contributes to the membrane crossing of a NC-NP as well as the self-resealing of the cell membrane after a NC-NP translocation. Our findings imply that NC-NPs can be delivered into a cell by combining applied electric field with membrane hyperpolarization/depolarization induced by an external stimulus.
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Affiliation(s)
- Yoko Ikeda
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Hideya Nakamura
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Shuji Ohsaki
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Satoru Watano
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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11
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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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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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Kitagawa T, Nishio T, Yoshikawa Y, Umezawa N, Higuchi T, Shew CY, Kenmotsu T, Yoshikawa K. Effects of Structural Isomers of Spermine on the Higher-Order Structure of DNA and Gene Expression. Int J Mol Sci 2021; 22:ijms22052355. [PMID: 33652986 PMCID: PMC7956460 DOI: 10.3390/ijms22052355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest for TSPM among spermine isomers. A numerical evaluation of the strength of the interaction of these polyamines with negatively charged double-strand DNA revealed that this ordering of the potency corresponds to the order of the strength of the attractive interaction between phosphate groups of DNA and positively charged amino groups of the polyamines.
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Affiliation(s)
- Tomoki Kitagawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Takashi Nishio
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Yuko Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Chwen-Yang Shew
- Doctoral Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA;
- Department of Chemistry, College of Staten Island, Staten Island, New York, NY 10314, USA
| | - Takahiro Kenmotsu
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Correspondence: (T.K.); (K.Y.)
| | - Kenichi Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (T.K.); (K.Y.)
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14
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Caetano DLZ, de Carvalho SJ, Metzler R, Cherstvy AG. Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption-desorption transition boundary. J R Soc Interface 2020; 17:20200199. [PMID: 32574545 PMCID: PMC7328387 DOI: 10.1098/rsif.2020.0199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption-the phase-separation curve between the adsorbed and desorbed states of the PEs-as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE-SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption-desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.
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Affiliation(s)
- Daniel L. Z. Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, Campus São José do Rio Preto, 15054-000 Brazil
- Institute of Chemistry, State University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
- Center for Computational Engineering and Sciences, State University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
| | - Sidney J. de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, Campus São José do Rio Preto, 15054-000 Brazil
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G. Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, 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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Robertson DS. Human body cell membranes and antigen control. Med Hypotheses 2019; 135:109480. [PMID: 31778893 DOI: 10.1016/j.mehy.2019.109480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 11/18/2022]
Abstract
The variables involved in the initiation and operation of the human immune system are considered. It is shown that the number of variations associated with disease and other detrimental conditions exceeds the number of lymphocyte cells available for control of these conditions. It is proposed that the immune system functions by changes in the ionic strength of metabolic fluids which in turn control the formation and stability of cell membranes. The application of these conditions to the control of bacterial, virus particle and other antigens is detailed. Observations supporting the proposals are presented.
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Affiliation(s)
- D S Robertson
- 205, Pickersleigh Road, Malvern, Worcestershire, England WR14 2QS, United Kingdom.
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17
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Zinchenko A, Hiramatsu H, Yamaguchi H, Kubo K, Murata S, Kanbe T, Hazemoto N, Yoshikawa K, Akitaya T. Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription. Biophys J 2019; 116:1836-1844. [PMID: 31076102 PMCID: PMC6531782 DOI: 10.1016/j.bpj.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 04/12/2019] [Indexed: 02/04/2023] Open
Abstract
Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan.
| | - Hiroyuki Hiramatsu
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | | | - Koji Kubo
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Shizuaki Murata
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Toshio Kanbe
- Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Norio Hazemoto
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuo Akitaya
- Department of Chemistry, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
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18
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Luque-Caballero G, Maldonado-Valderrama J, Quesada-Pérez M, Martín-Molina A. Interaction of DNA with likely-charged lipid monolayers: An experimental study. Colloids Surf B Biointerfaces 2019; 178:170-176. [PMID: 30856586 DOI: 10.1016/j.colsurfb.2019.02.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/31/2022]
Abstract
Anionic lipids are increasingly being used in lipoplexes for synthetic gene vectors as an alternative to cationic lipids. This is primarily due to their lower toxicity, which makes them biocompatible and adaptable to be tissue specific. However, anionic lipoplexes require the presence of multivalent cations to promote the electrostatic attraction between DNA and anionic lipid mono- and bilayers. In this work we provide for the first time experimental results of the adsorption of linear DNA onto anionic/zwitterionic lipid monolayers without any addition of cations. This is demonstrated experimentally by means of Langmuir monolayers of DOPE/DOPG (1:1) lipids spread on a water subphase that contains calf thymus DNA. The adsorption of DNA onto anionic/zwitterionic lipid monolayers is discussed in terms of the surface pressure-molecular area isotherms recorded in the absence and in the presence of different electrolytes. Measurements of the surface potential provide additional evidence of the different interaction of DNA anionic/zwitterionic lipid monolayers depending on the presence and nature of electrolyte. These experimental results are further analysed in terms of the overall dipole moment normal to the monolayers providing new insight into the behaviour of anionic lipoplexes and the role of zwitterionic lipids.
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Affiliation(s)
- German Luque-Caballero
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain
| | - Julia Maldonado-Valderrama
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain; Unidad de excelencia "Modelling Nature" (MNat), Universidad de Granada, Spain
| | - Manuel Quesada-Pérez
- Departamento de Física, Escuela Politécnica Superior de Linares, Universidad de Jaén, 23700, Linares, Jaén, Spain
| | - Alberto Martín-Molina
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain; Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Spain.
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19
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Liu KT, Ran SY. Multistage dynamics of Hg 2+-DNA interactions: a single-molecule study. Phys Chem Chem Phys 2019; 21:2919-2928. [PMID: 30675618 DOI: 10.1039/c8cp07399f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The metal ion-DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T-Hg2+-T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanism has not been fully understood. In the present study, we used magnetic tweezers to explore the interactions between λ-DNA and two metal ions, Hg2+ and Cd2+, at the single-molecule level. Both metal ions caused considerable DNA conformational changes. The resulting DNA compaction dynamics were related to the ion concentration and the exerted force. The increase in the ion concentration promoted DNA compaction, whereas exerting greater forces inhibited this process. Application of a high force generated two-stage dynamics of the Hg2+-DNA interaction. However, at a sufficiently high Hg2+ concentration, a lower force led to a three-stage process. In contrast, the curves of the binding of Cd2+ ions to DNA had a stepwise pattern. Both the AFM scanning results and the single-molecule measurements confirmed that Hg2+ influences the DNA conformation in a more pronounced manner than Cd2+. The multistage Hg2+-DNA interaction was considered to be a result of the different binding mechanisms, including the mismatched base-pair formation. A model was then proposed to explain the peculiar dynamics.
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Affiliation(s)
- Kang-Tao Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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20
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Angelescu DG. Coarse-grained simulation studies on the adsorption of polyelectrolyte complexes upon lipid membranes. Phys Chem Chem Phys 2019; 21:12446-12459. [DOI: 10.1039/c9cp01448a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conformations of a polyelectrolyte complex irreversibly bound to a zwitterionic lipid bilayer.
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Affiliation(s)
- Daniel G. Angelescu
- Romanian Academy
- “Ilie Murgulescu” Institute of Physical Chemistry
- 060021 Bucharest
- Romania
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21
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Nakamura H, Sezawa K, Hata M, Ohsaki S, Watano S. Direct translocation of nanoparticles across a model cell membrane by nanoparticle-induced local enhancement of membrane potential. Phys Chem Chem Phys 2019; 21:18830-18838. [DOI: 10.1039/c9cp02935d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nanoparticles directly translocate across a cell membrane by a locally enhanced membrane potential at the NP/cell-membrane contact interface.
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Affiliation(s)
- Hideya Nakamura
- Department of Chemical Engineering
- Osaka Prefecture University
- Osaka 599-8531
- Japan
| | - Kyohei Sezawa
- Department of Chemical Engineering
- Osaka Prefecture University
- Osaka 599-8531
- Japan
| | - Masataka Hata
- Department of Chemical Engineering
- Osaka Prefecture University
- Osaka 599-8531
- Japan
| | - Shuji Ohsaki
- Department of Chemical Engineering
- Osaka Prefecture University
- Osaka 599-8531
- Japan
| | - Satoru Watano
- Department of Chemical Engineering
- Osaka Prefecture University
- Osaka 599-8531
- Japan
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22
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Huang B, Tan Z, Bohinc K, Zhang S. Interaction between nanoparticles and charged phospholipid membranes. Phys Chem Chem Phys 2018; 20:29249-29263. [PMID: 30427341 DOI: 10.1039/c8cp04740e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Charged lipids in cell membranes and subcellular organelles are arranged in the form of a bilayer with the hydrocarbon tails sequestered away from the water and the polar head groups exposed to the aqueous environment. Most of them bear net negative charges leading to the negatively charged cell membranes. Charged lipid-lipid and lipid-protein interactions are generally dynamic and heavily depend on their local molecular concentrations. To examine the electrostatic properties of charged lipid layers in contact with an electrolyte solution, we incorporate the single chain mean field theory with Poisson-Boltzmann theory to explore the equilibrium structure of charged phospholipid membranes. Using the three bead coarse-grained model we reproduced the essential equilibrium properties of the charged phospholipid bilayer. We also investigate the influence of the mobile ions on the thickness of the layer, the area per lipid (APL), and the electrostatic potential of the membrane. Then we investigate the attraction-repulsion property of two charged nanoparticles which are stuck on the charged lipid molecules surrounded with mobile ions. After that we simulated the interaction between the Pleckstrin homology domain (PH domain) of Akt and the cytoplasmic membrane. Taking into account the electrostatic interaction, we observe the structure changes of the membrane at different concentrations of mobile ions in its equilibrium state. Also we discuss the influence of mobile ions on the size of the pore opened in the membrane by the charged protein. Such an observation may shed light on the activation of oncogenic Akt (or protein kinase B) around the membrane at the molecular level.
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Affiliation(s)
- Beibei Huang
- Intelligent Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, 1901 East Road, Houston, TX 77054, USA.
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23
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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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24
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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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25
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Abstract
What are the features of partitioning of crystalline materials on the surface of a two-component icosahedral vesicle? We model the response of the rigid hardly stretchable crystalline icosahedra upon addition of a softer component on its surface. We demonstrate how the soft phase "invades" the shell regions with the highest elastic energy density around 12 5-fold topological defects. We explore the phase diagram of these inhomogeneous shells as a function of the soft material fraction, shell radius, and elastic moduli of the two phases. The findings are compared with the recent computer simulation findings, and their biological relevance, for example, for the structure of icosahedral viruses, is also discussed.
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Affiliation(s)
- Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany.,IAS-2 Institute, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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26
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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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27
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Luque-Caballero G, Maldonado-Valderrama J, Quesada-Pérez M, Martín-Molina A. Atomic force microscopy as a tool to study the adsorption of DNA onto lipid interfaces. Microsc Res Tech 2016; 80:11-17. [PMID: 27014963 DOI: 10.1002/jemt.22654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/25/2016] [Accepted: 02/05/2016] [Indexed: 11/08/2022]
Abstract
The Atomic Force Microscopy (AFM) technique appears as a central tool for the characterization of DNA adsorption onto lipid interfaces. Regardless of the huge number of surveys devoted to this issue, there are still fascinating phenomena in this field that have not been explored in detail by AFM. For instance, adsorption of DNA onto like-charged lipid surfaces mediated by cations is still not fully understood even though it is gaining popularity nowadays in gene therapy and nanotechnology. Studies related to the complexation of DNA with anionic lipids as a non-viral gene delivery vehicle as well as the formation of self-assembled nanoscale DNA constructs (DNA origami) are two of the most attractive systems. Unfortunately, molecular mechanisms underlying the adsorption of DNA onto anionic lipid interfaces remain unclear so far. In view of that, AFM becomes an appropriate technique to provide valuable information to understand the adsorption of DNA to anionic lipid surfaces. As a second part of this review we provide an illustrative example of application of the AFM technique to probe the DNA adsorption onto a model lipid monolayer negatively charged. Microsc. Res. Tech. 80:11-17, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Germán Luque-Caballero
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
| | - Julia Maldonado-Valderrama
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
| | - Manuel Quesada-Pérez
- Departamento de Física, Escuela Politécnica Superior de Linares, Universidad de Jaén, Linares, Jaén, 23700, Spain
| | - Alberto Martín-Molina
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, Granada, 18071, Spain
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28
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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: 126] [Impact Index Per Article: 15.8] [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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29
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Salt-induced reentrant stability of polyion-decorated particles with tunable surface charge density. Colloids Surf B Biointerfaces 2016; 137:109-20. [DOI: 10.1016/j.colsurfb.2015.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 01/17/2023]
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30
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Ghosh SK, Cherstvy AG, Metzler R. Deformation propagation in responsive polymer network films. J Chem Phys 2014; 141:074903. [DOI: 10.1063/1.4893056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Surya K. Ghosh
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G. Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Department of Physics, Tampere University of Technology, 33101 Tampere, Finland
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The Role of the Actin Cytoskeleton and Lipid Rafts in the Localization and Function of the ABCC1 Transporter. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/105898] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ATP-binding cassette (ABC) transporters are known to be important factors in multidrug resistance of tumor cells. Lipid rafts have been implicated in their localization in the plasma membrane, where they function as drug efflux pumps. This specific localization in rafts may support the activity of ABC/Abc transporters. This raises questions regarding the nature and composition of the lipid rafts that harbor ABC/Abc transporters and the dependence of ABC/Abc transporters—concerning their localization and activity—on lipid raft constituents. Here we review our work of the past 10 years aimed at evaluating whether ABC/Abc transporters are dependent on a particular membrane environment for their function. What is the nature of this membrane environment and which of the lipid raft constituents are important for this dependency? It turns out that cortical actin is of major importance for stabilizing the localization and function of the ABC/Abc transporter, provided it is localized in an actin-dependent subtype of lipid rafts, as is the case for human ABCC1/multidrug resistance-related protein 1 (MRP1) and rodent Abcc1/Mrp1 but not human ABCB1/P-glycoprotein (PGP). On the other hand, sphingolipids do not appear to be modulators of ABCC1/MRP1 (or Abcc1/Mrp1), even though they are coregulated during drug resistance development.
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Cherstvy AG. Electrostatics and Charge Regulation in Polyelectrolyte Multilayered Assembly. J Phys Chem B 2014; 118:4552-60. [DOI: 10.1021/jp502460v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Andrey G. Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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de Carvalho SJ, Metzler R, Cherstvy AG. Critical adsorption of polyelectrolytes onto charged Janus nanospheres. Phys Chem Chem Phys 2014; 16:15539-50. [DOI: 10.1039/c4cp02207f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conditions of critical polyelectrolyte adsorption onto spherical charged Janus nano-particles are exploited by Monte-Carlo computer simulations and theoretically.
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Affiliation(s)
| | - Ralf Metzler
- Institute for Physics and Astronomy
- University of Potsdam
- Potsdam-Golm, Germany
- Department of Physics
- Tampere University of Technology
| | - Andrey G. Cherstvy
- Institute for Physics and Astronomy
- University of Potsdam
- Potsdam-Golm, Germany
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