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De Nicola A, Montis C, Donati G, Molinaro A, Silipo A, Balestri A, Berti D, Di Lorenzo F, Zhu YL, Milano G. Bacterial lipids drive compartmentalization on the nanoscale. NANOSCALE 2023; 15:8988-8995. [PMID: 37144495 PMCID: PMC10210972 DOI: 10.1039/d3nr00559c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023]
Abstract
The design of cellular functions in synthetic systems, inspired by the internal partitioning of living cells, is a constantly growing research field that is paving the way to a large number of new remarkable applications. Several hierarchies of internal compartments like polymersomes, liposomes, and membranes are used to control the transport, release, and chemistry of encapsulated species. However, the experimental characterization and the comprehension of glycolipid mesostructures are far from being fully addressed. Lipid A is indeed a glycolipid and the endotoxic part of Gram-negative bacterial lipopolysaccharide; it is the moiety that is recognized by the eukaryotic receptors giving rise to the modulation of innate immunity. Herein we propose, for the first time, a combined approach based on hybrid Particle-Field (hPF) Molecular Dynamics (MD) simulations and Small Angle X-Ray Scattering (SAXS) experiments to gain a molecular picture of the complex supramolecular structures of lipopolysaccharide (LPS) and lipid A at low hydration levels. The mutual support of data from simulations and experiments allowed the unprecedented discovery of the presence of a nano-compartmentalized phase composed of liposomes of variable size and shape which can be used in synthetic biological applications.
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Affiliation(s)
- Antonio De Nicola
- Scuola Superiore Meridionale, Via Largo San Marcellino 10, 80132 Napoli, Italy
- Graduate School of Organic Materials Science, Yamagata, University, Jonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan
| | - Costanza Montis
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Greta Donati
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - Alba Silipo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - Arianna Balestri
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Debora Berti
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze and CSGI, 50019 Firenze, Italy.
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy.
| | - You-Liang Zhu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130021, China
| | - Giuseppe Milano
- University of Naples Federico II, Department of Chemical, Materials and Production Engineering, Piazzale V. Tecchio, 80, 80125 Napoli, Italy.
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2
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Singhal A, Agur Sevink GJ. The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study. NANOSCALE ADVANCES 2021; 3:6635-6648. [PMID: 36132649 PMCID: PMC9417560 DOI: 10.1039/d1na00578b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/16/2021] [Indexed: 05/09/2023]
Abstract
Understanding the uptake of nanoparticles (NPs) by different types of cellular membranes plays a pivotal role in the design of NPs for medical applications and in avoiding adverse effects that result in nanotoxicity. Yet, the role of key design parameters, such as the bare NP material, NP size and surface reactivity, and the nature of NP coatings, in membrane remodelling and uptake mechanisms is still very poorly understood, particularly towards the lower range of NP dimensions that are beyond the experimental imaging resolution. The same can be said about the role of a particular membrane composition. Here, we systematically employ biased and unbiased molecular dynamics simulations to calculate the binding energy for three bare materials (Ag/SiO2/TiO2) and three NP sizes (1/3/5 nm diameter) with a representative lung surfactant membrane, and to study their binding kinetics. The calculated binding energies show that irrespective of size, Ag nanoparticles bind very strongly to the bilayer, while the NPs made of SiO2 or TiO2 experience very low to no binding. The unbiased simulations provide insight into how the NPs and membrane affect each other in terms of the solvent-accessible surface area (SASA) of the NPs and the defect types and fluidity of the membrane. Using these systematic fine-grained results in coarsening procedures will pave the way for simulations considering NP sizes that are well beyond the membrane thickness, i.e. closer to experimental dimensions, for which different binding characteristics and more significant membrane remodelling are expected.
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Affiliation(s)
- Ankush Singhal
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - G J Agur Sevink
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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3
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Adsorption immobilization of biomolecules from subphase on Langmuir monolayers of organo-modified single-walled carbon nanotube. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126559] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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4
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Kazakov AD, Prokacheva VM, Uhlík F, Košovan P, Leermakers FAM. Computer modeling of polymer stars in variable solvent conditions: a comparison of MD simulations, self-consistent field (SCF) modeling and novel hybrid Monte Carlo SCF approach. SOFT MATTER 2021; 17:580-591. [PMID: 33200761 DOI: 10.1039/d0sm01080d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Computer-aided modeling is a systematic approach to grasp the physics of macromolecules, but it remains essential to know when to trust the results and when not. For a polymer star, we consider three approaches: (i) Molecular Dynamics (MD) simulations and implementing a coarse-grained model, (ii) the self-consistent field approach based on a mean-field approximation and implementing the lattice model due to Scheutjens and Fleer (SF-SCF) and (iii) novel hybrid Monte Carlo self-consistent field (MC-SCF) method, which combines a coarse-grained model driven by a Monte Carlo method and a mean-field representation driven by SF-SCF. We compare the performance of these approaches under a wide range of solvent qualities. The MD approach is formally the most exact but suffers from reasonable convergence. The mean-field approach works similarly in all solvent qualities but is quantitatively least accurate. The MC-SCF hybrid allows us to combine the benefits of the simulation route and the effective performance of SCF. We consider the center-to-end distance Rce, the radius of gyration Rg2 of the star and the polymer density profiles φ(r) of polymer-segments in it. All three methods show a good qualitative agreement one to another. The MC-SCF method is in good agreement with the scaling predictions in the whole range of solvent quality values showing that it grasps the essential physics while remaining computationally in bounds.
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Affiliation(s)
- Alexander D Kazakov
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Varvara M Prokacheva
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Filip Uhlík
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Peter Košovan
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Frans A M Leermakers
- Department of Agrotechnology and Food Sciences, Wageningen University and Research Center, Wageningen, The Netherlands
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5
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Uehara TM, Cancino-Bernardi J, Miranda PB, Zucolotto V. Investigating the interactions of corona-free SWCNTs and cell membrane models using sum-frequency generation. SOFT MATTER 2020; 16:5711-5717. [PMID: 32525195 DOI: 10.1039/d0sm00256a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of the interactions between biomolecules and nanomaterials is of great importance in many areas of nanomedicine and bioapplications. Numerous studies in this area have been performed. However, toxicological aspects involving the interaction between phospholipids and carbon nanotubes (CNTs) remain undefined, especially for those cases in which a protein corona is not formed around the nanomaterial (corona-free nanomaterials). This study focuses on the interaction of Langmuir films of dipalmitoylphosphatidylglycerol (DPPG) and dipalmitoylphosphatidylcholine (DPPC) with corona-free, single-walled CNTs. Surface pressure-area isotherms and sum-frequency generation (SFG) vibrational spectroscopy, a non-linear optical technique used to study surfaces and interfaces, were used to investigate the lipid tail orientation and conformation, aiming to understand the interactions between phospholipids and single walled carbon nanotubes functionalized by carboxylic acid (SWCNTs-COOH) at the air-water interface under low ionic strength conditions. Data from isotherms and SFG spectra revealed that the SWCNT adsorption at the air-water interface is induced by the presence of both lipids, although at a lesser extent for DPPG due to its anionic head group, which could result in repulsion of SWCNTs-COOH that also bear a negative charge. Furthermore, lipid monolayers remained conformationally ordered, indicating insertion of SWCNTs into the lipid monolayer. Our results corroborate previous works and simulations in the literature, but made it possible to perform an in-depth investigation of the interaction of these nanomaterials with components of phospholipid membranes.
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Affiliation(s)
- Thiers Massami Uehara
- Nanomedicine and Nanotoxicology Group, University of São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil.
| | - Juliana Cancino-Bernardi
- Nanomedicine and Nanotoxicology Group, University of São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil.
| | - Paulo Barbeitas Miranda
- Polymer Group "Prof. Bernhard Gross", Physics Institute of São Carlos, University of São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil
| | - Valtencir Zucolotto
- Nanomedicine and Nanotoxicology Group, University of São Paulo, CP 369, São Carlos, São Paulo 13560-970, Brazil.
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6
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Aggregation of Lipid A Variants: A Hybrid Particle-Field Model. Biochim Biophys Acta Gen Subj 2020; 1865:129570. [PMID: 32105775 DOI: 10.1016/j.bbagen.2020.129570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/23/2022]
Abstract
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates.
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7
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Pfeiffer T, De Nicola A, Montis C, Carlà F, van der Vegt NFA, Berti D, Milano G. Nanoparticles at Biomimetic Interfaces: Combined Experimental and Simulation Study on Charged Gold Nanoparticles/Lipid Bilayer Interfaces. J Phys Chem Lett 2019; 10:129-137. [PMID: 30563321 DOI: 10.1021/acs.jpclett.8b03399] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The poor understanding of the interaction of nanomaterials with biologically relevant interfaces is recognized as one of the major issues currently limiting the development of nanomedicine. The central purpose of this study is to compare experimental (confocal microscopy, fluorescence correlation spectroscopy, X-ray reflectivity) and computational (molecular dynamics simulations) results to thoroughly describe the interaction of cationic gold nanoparticles (AuNPs) with mixed zwitterionic/anionic lipid membranes. The adhesion of AuNPs to the lipid membrane is investigated on different length scales from a structural and dynamical point of view; with this approach, a series of complex phenomena, spanning from lipid extraction, localized membrane disruption, lateral phase separation, and slaved diffusion, are characterized and interpreted from a molecular level to macroscopic observations.
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Affiliation(s)
- Tobias Pfeiffer
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Antonio De Nicola
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
| | - Costanza Montis
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Francesco Carlà
- European Synchrotron Radiation Facility , CS 40220 , Grenoble Cedex 9, France
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie , Technische Universität Darmstadt , Alarich-Weiss-Straße 10 , Darmstadt 64289 , Germany
| | - Debora Berti
- Department of Chemistry "Ugo Schiff" and CSGI , University of Florence , via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy
| | - Giuseppe Milano
- Department of Organic Materials Science , Yamagata University , 4-3-16 Jonan Yonezawa , Yamagata-ken 992-8510 , Japan
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8
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Bore SL, Milano G, Cascella M. Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains. J Chem Theory Comput 2018; 14:1120-1130. [DOI: 10.1021/acs.jctc.7b01160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
| | - Giuseppe Milano
- Department
of Organic Materials Science, University of Yamagata, 4-3-16 Jonan
Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo, Norway
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9
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Vögele M, Köfinger J, Hummer G. Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discuss 2018; 209:341-358. [DOI: 10.1039/c8fd00011e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
- Institute for Biophysics
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10
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Al-Qattan MN, Deb PK, Tekade RK. Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery. Drug Discov Today 2017; 23:235-250. [PMID: 29031623 DOI: 10.1016/j.drudis.2017.10.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Accepted: 10/05/2017] [Indexed: 01/05/2023]
Abstract
The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.
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Affiliation(s)
- Mohammed N Al-Qattan
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O. Box (1), Philadelphia University (19392), Jordan
| | - Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O. Box (1), Philadelphia University (19392), Jordan.
| | - Rakesh K Tekade
- National Institute of Pharmaceutical Education and Research (NIPER) Ahmedabad, (An Institute of National Importance, Government of India), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opposite Air Force Station, Gandhinagar, Gujarat 382355, India
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11
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Xie LQ, Liu YZ, Xi ZH, Li HY, Liang SD, Zhu KL. Computer simulations of the interaction of fullerene clusters with lipid membranes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1332410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Li-qiang Xie
- Department of Physics, Gansu Normal University for Nationalities, Hezuo, China
| | - Yong-zhi Liu
- Department of Physics, Gansu Normal University for Nationalities, Hezuo, China
| | - Zhong-hong Xi
- Department of Physics, Gansu Normal University for Nationalities, Hezuo, China
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou, China
| | - Hai-yi Li
- Department of Physics, Gansu Normal University for Nationalities, Hezuo, China
| | - Sheng-de Liang
- Department of Physics, Gansu Normal University for Nationalities, Hezuo, China
- Key Laboratory of Modern Acoustics, Ministry of Education, Institute of Acoustics, Nanjing University, Nanjing, China
| | - Kai-li Zhu
- Department of Chemistry, Gansu Normal University for Nationalities, Hezuo, China
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12
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Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G. Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS NANO 2017; 11:1273-1280. [PMID: 28103440 DOI: 10.1021/acsnano.6b05434] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Stephanie M Linker
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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13
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Kuku G, Saricam M, Akhatova F, Danilushkina A, Fakhrullin R, Culha M. Surface-Enhanced Raman Scattering to Evaluate Nanomaterial Cytotoxicity on Living Cells. Anal Chem 2016; 88:9813-9820. [PMID: 27611981 DOI: 10.1021/acs.analchem.6b02917] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The increasing number of reports about false positive or negative results from conventional cytotoxicity assays of nanomaterials (NMs) suggests that more reliable NM toxicity assessment methods should be developed. Here, we report a novel approach for nanotoxicity evaluation based on surface-enhanced Raman spectroscopy (SERS). Three model NMs were tested on two model cell lines and the results were validated by WST-1 cytotoxicity assay and annexin V-FITC/propidium iodide (PI) staining as apoptosis-necrosis assay. The localization of nanoparticles (NPs) in the cells and the cellular conditions upon NP incubation were visualized by transmission electron microscopy (TEM) and enhanced dark-field (EDF) microscopy. SERS revealed a broader view on the consequences of cell-NM interactions compared to the conventional cytotoxicity assays where only one aspect of toxicity can be measured by one assay type. The results suggest that SERS can significantly contribute to the cytotoxicity evaluation bypassing NM or assay component-related complications with less effort.
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Affiliation(s)
- Gamze Kuku
- Department of Genetics and Bioengineering, Yeditepe University , Atasehir, Istanbul, 34755, Turkey
| | - Melike Saricam
- Department of Genetics and Bioengineering, Yeditepe University , Atasehir, Istanbul, 34755, Turkey
| | - Farida Akhatova
- Bionanotechnology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University , Kreml uramı 18, Kazan, Republic of Tatarstan, 420008, Russian Federation
| | - Anna Danilushkina
- Bionanotechnology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University , Kreml uramı 18, Kazan, Republic of Tatarstan, 420008, Russian Federation
| | - Rawil Fakhrullin
- Bionanotechnology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University , Kreml uramı 18, Kazan, Republic of Tatarstan, 420008, Russian Federation
| | - Mustafa Culha
- Department of Genetics and Bioengineering, Yeditepe University , Atasehir, Istanbul, 34755, Turkey
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14
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Tran IC, Tunuguntla RH, Kim K, Lee JRI, Willey TM, Weiss TM, Noy A, van Buuren T. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study. NANO LETTERS 2016; 16:4019-4024. [PMID: 27322135 DOI: 10.1021/acs.nanolett.6b00466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. In order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers. Our results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs.
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Affiliation(s)
- Ich C Tran
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Ramya H Tunuguntla
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Kyunghoon Kim
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Jonathan R I Lee
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Trevor M Willey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center , Menlo Park, California 94025, United States
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Tony van Buuren
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
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15
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Bulacu M, Sevink GJA. Erratum. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1716-25. [PMID: 26273716 DOI: 10.1016/j.bbamem.2015.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid–polymer–oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precedes fusion.
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Bulacu M, Sevink GJA. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:848-58. [PMID: 25528473 DOI: 10.1016/j.bbamem.2014.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/03/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid-polymer-oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide-pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precede fusion.
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Affiliation(s)
- M Bulacu
- Culgi BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - G J A Sevink
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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De Nicola A, Kawakatsu T, Milano G. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:5651-67. [PMID: 26583248 DOI: 10.1021/ct500492h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.
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Affiliation(s)
- Antonio De Nicola
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno , via Ponte don Melillo, Fisciano, Salerno I-84085, Italy.,IMAST Scarl-Technological District in Polymer and Composite Engineering, Piazza Bovio 22, Napoli, Napoli I-80133, Italy
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University , Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università degli Studi di Salerno , via Ponte don Melillo, Fisciano, Salerno I-84085, Italy.,IMAST Scarl-Technological District in Polymer and Composite Engineering, Piazza Bovio 22, Napoli, Napoli I-80133, Italy
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