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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS APPLIED BIO MATERIALS 2024; 7:528-534. [PMID: 36070609 PMCID: PMC10880049 DOI: 10.1021/acsabm.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.
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Affiliation(s)
- Martin Vögele
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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2
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Brosio G, Rossi G, Bochicchio D. Nanoparticle-induced biomembrane fusion: unraveling the effect of core size on stalk formation. NANOSCALE ADVANCES 2023; 5:4675-4680. [PMID: 37705778 PMCID: PMC10496904 DOI: 10.1039/d3na00430a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/01/2023] [Indexed: 09/15/2023]
Abstract
Membrane fusion in vitro is a strategy to load model or cell-derived vesicles with proteins, drugs, and genetic materials for theranostic applications. It is thus crucial to develop strategies to control the fusion process, also through synthetic fusogenic agents. Ligand-protected, membrane-penetrating gold nanoparticles (Au NPs) can facilitate membrane fusion, but the molecular mechanisms remain unresolved. Here, we tackle NP-induced stalk formation using a coarse-grained molecular dynamics approach and enhanced sampling techniques. We show that smaller (2 nm in diameter) NPs lead to a lower free energy barrier and higher stalk stability than larger NPs (4 nm). We demonstrate that this difference is due to a different ligand conformational freedom, which in turn depends on the Au core curvature. Our study provides precious insights into the mechanisms underlying NP-mediated membrane fusion, while our computational approach is general and applicable to studying stalk formation caused by other fusogenic agents.
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Affiliation(s)
- Giorgia Brosio
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
| | - Giulia Rossi
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
| | - Davide Bochicchio
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
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Qiu C, Xia F, Zhang J, Shi Q, Meng Y, Wang C, Pang H, Gu L, Xu C, Guo Q, Wang J. Advanced Strategies for Overcoming Endosomal/Lysosomal Barrier in Nanodrug Delivery. RESEARCH (WASHINGTON, D.C.) 2023; 6:0148. [PMID: 37250954 PMCID: PMC10208951 DOI: 10.34133/research.0148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
Nanocarriers have therapeutic potential to facilitate drug delivery, including biological agents, small-molecule drugs, and nucleic acids. However, their efficiency is limited by several factors; among which, endosomal/lysosomal degradation after endocytosis is the most important. This review summarizes advanced strategies for overcoming endosomal/lysosomal barriers to efficient nanodrug delivery based on the perspective of cellular uptake and intracellular transport mechanisms. These strategies include promoting endosomal/lysosomal escape, using non-endocytic methods of delivery to directly cross the cell membrane to evade endosomes/lysosomes and making a detour pathway to evade endosomes/lysosomes. On the basis of the findings of this review, we proposed several promising strategies for overcoming endosomal/lysosomal barriers through the smarter and more efficient design of nanodrug delivery systems for future clinical applications.
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Affiliation(s)
- Chong Qiu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fei Xia
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junzhe Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiaoli Shi
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuqing Meng
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huanhuan Pang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Liwei Gu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chengchao Xu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiuyan Guo
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
- Department of Nephrology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital,
Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
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4
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Hatamie A, He X, Zhang XW, Oomen PE, Ewing AG. Advances in nano/microscale electrochemical sensors and biosensors for analysis of single vesicles, a key nanoscale organelle in cellular communication. Biosens Bioelectron 2022; 220:114899. [DOI: 10.1016/j.bios.2022.114899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
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Precise Design Strategies of Nanotechnologies for Controlled Drug Delivery. J Funct Biomater 2022; 13:jfb13040188. [PMID: 36278656 PMCID: PMC9590086 DOI: 10.3390/jfb13040188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Rapid advances in nanotechnologies are driving the revolution in controlled drug delivery. However, heterogeneous barriers, such as blood circulation and cellular barriers, prevent the drug from reaching the cellular target in complex physiologic environments. In this review, we discuss the precise design of nanotechnologies to enhance the efficacy, quality, and durability of drug delivery. For drug delivery in vivo, drugs loaded in nanoplatforms target particular sites in a spatial- and temporal-dependent manner. Advances in stimuli-responsive nanoparticles and carbon-based drug delivery platforms are summarized. For transdermal drug delivery systems, specific strategies including microneedles and hydrogel lead to a sustained release efficacy. Moreover, we highlight the current limitations of clinical translation and an incentive for the future development of nanotechnology-based drug delivery.
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull MT, Hagen WJH, Hummer G, Kosinski J, Beck M. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 2022; 376:eabm9506. [PMID: 35679397 DOI: 10.1126/science.abm9506] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg-est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf-fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma-tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal-lenge for structural biologists. RATIONALE Considerable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra-tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc-tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf-fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight-forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol-ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination. RESULTS In this study, we used artificial intelligence (AI)-based prediction to generate an exten-sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac-terized. Benchmarking against previous and unpublished x-ray and cryo-electron micros-copy structures revealed unprecedented accu-racy. We obtained well-resolved cryo-electron tomographic maps of both the constricted and dilated conformational states of the hu-man NPC. Using integrative modeling, we fit-ted the structural models of individual NUPs into the cryo-electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf-fold. We elucidated in great detail how mem-brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en-vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension. CONCLUSION Our 70-MDa atomically re-solved model covers >90% of the human NPC scaffold. It captures conforma-tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy-namic model of the NPC. Our study exempli-fies how AI-based structure prediction may accelerate the elucidation of subcellular ar-chitecture at atomic resolution. [Figure: see text].
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Affiliation(s)
- Shyamal Mosalaganti
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany
| | - Marc Siggel
- European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Reiya Taniguchi
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christian E Zimmerli
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katarzyna Buczak
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Florian H Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Erica Margiotta
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marie-Therese Mackmull
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany.,Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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8
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Zhang J, Wang Y, Wang J, Yan Y, Li J, Li Z. Self-assembly of an in silico designed dipeptide derivative to obtain photo-responsive vesicles. Phys Chem Chem Phys 2022; 24:27751-27758. [DOI: 10.1039/d2cp03258a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photo-responsive vesicles self-assembled from in silico designed peptide derivatives were investigated using coarse-grained molecular dynamics simulations.
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Affiliation(s)
- Jun Zhang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Yining Wang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Junfeng Wang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Youguo Yan
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jiawei Li
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
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9
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Hatamie A, Ren L, Zhang X, Ewing AG. Vesicle Impact Electrochemical Cytometry to Determine Carbon Nanotube-Induced Fusion of Intracellular Vesicles. Anal Chem 2021; 93:13161-13168. [PMID: 34499839 PMCID: PMC8495673 DOI: 10.1021/acs.analchem.1c01462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon nanotube (CNT)-modified electrodes are used to obtain new measurements of vesicle content via amperometry. We have investigated the interaction between CNTs and isolated adrenal chromaffin vesicles (as a model) by vesicle impact electrochemical cytometry. Our data show that the presence of CNTs not only significantly increased the vesicular catecholamine number from 2,250,000 ± 112,766 molecules on a bare electrode to 3,880,000 ± 686,573 molecules on CNT/carbon fiber electrodes but also caused an enhancement in the maximum intensity of the current, which implies the existence of strong interactions between vesicle biolayers and CNTs and an altered electroporation process. We suggest that CNTs might perturb and destabilize the membrane structure of intracellular vesicles and cause the aggregation or fusion of vesicles into new vesicles with larger size and higher content. Our findings are consistent with previous computational and experimental results and support the hypothesis that CNTs as a mediator can rearrange the phospholipid bilayer membrane and trigger homotypic fusion of intracellular vesicles.
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Affiliation(s)
- Amir Hatamie
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Lin Ren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Xinwei Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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10
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Cino EA, Borbuliak M, Hu S, Tieleman DP. Lipid distributions and transleaflet cholesterol migration near heterogeneous surfaces in asymmetric bilayers. Faraday Discuss 2021; 232:103-113. [PMID: 34549760 DOI: 10.1039/d1fd00003a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Specific and nonspecific protein-lipid interactions in cell membranes have important roles in an abundance of biological functions. We have used coarse-grained (CG) molecular dynamics (MD) simulations to assess lipid distributions and cholesterol flipping dynamics around surfaces in a model asymmetric plasma membrane containing one of six structurally distinct entities: aquaporin-1 (AQP1), the bacterial β-barrel outer membrane proteins OmpF and OmpX, the KcsA potassium channel, the WALP23 peptide and a carbon nanotube (CNT). Our findings revealed varied lipid partitioning and cholesterol flipping times around the different solutes and putative cholesterol binding sites in AQP1 and KcsA. The results suggest that protein-lipid interactions can be highly variable, and that surface-dependent lipid profiles are effectively manifested in CG simulations with the Martini force field.
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Affiliation(s)
- Elio A Cino
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada. .,Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mariia Borbuliak
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - Shangnong Hu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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Holdbrook DA, Marzinek JK, Boncel S, Boags A, Tan YS, Huber RG, Verma CS, Bond PJ. The nanotube express: Delivering a stapled peptide to the cell surface. J Colloid Interface Sci 2021; 604:670-679. [PMID: 34280765 DOI: 10.1016/j.jcis.2021.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/23/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
Abstract
HYPOTHESIS Carbon nanotubes (CNTs) represent a novel platform for cellular delivery of therapeutic peptides. Chemically-functionalized CNTs may enhance peptide uptake by improving their membrane targeting properties. EXPERIMENTS Using coarse-grained (CG) molecular dynamics (MD) simulations, we investigate membrane interactions of a peptide conjugated to pristine and chemically-modified CNTs. As proof of principle, we focus on their interactions with PM2, an amphipathic stapled peptide that inhibits the E3 ubiquitin ligase HDM2 from negatively regulating the p53 tumor suppressor. CNT interaction with both simple planar lipid bilayers as well as spherical lipid vesicles was studied, the latter as a surrogate for curved cellular membranes. FINDINGS Membrane permeation was rapid and spontaneous for both pristine and oxidized CNTs when unconjugated. This was slowed upon addition of a noncovalently attached peptide surface "sheath", which may be an effective way to slow CNT entry and avert membrane rupture. The CNT conjugates were observed to "desheath" their peptide layer at the bilayer interface upon insertion, leaving their cargo behind in the outer leaflet. This suggests that a synergy may exist to optimize CNT safety whilst enhancing the delivery efficiency of "hitchhiking" therapeutic molecules.
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Affiliation(s)
- Daniel A Holdbrook
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Slawomir Boncel
- Silesian University of Technology, Faculty of Chemistry, Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Alister Boags
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Roland G Huber
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, Singapore.
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore, Singapore.
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12
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Ho NT, Siggel M, Camacho KV, Bhaskara RM, Hicks JM, Yao YC, Zhang Y, Köfinger J, Hummer G, Noy A. Membrane fusion and drug delivery with carbon nanotube porins. Proc Natl Acad Sci U S A 2021; 118:e2016974118. [PMID: 33941689 PMCID: PMC8126853 DOI: 10.1073/pnas.2016974118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Drug delivery mitigates toxic side effects and poor pharmacokinetics of life-saving therapeutics and enhances treatment efficacy. However, direct cytoplasmic delivery of drugs and vaccines into cells has remained out of reach. We find that liposomes studded with 0.8-nm-wide carbon nanotube porins (CNTPs) function as efficient vehicles for direct cytoplasmic drug delivery by facilitating fusion of lipid membranes and complete mixing of the membrane material and vesicle interior content. Fusion kinetics data and coarse-grained molecular dynamics simulations reveal an unusual mechanism where CNTP dimers tether the vesicles, pull the membranes into proximity, and then fuse their outer and inner leaflets. Liposomes containing CNTPs in their membranes and loaded with an anticancer drug, doxorubicin, were effective in delivering the drug to cancer cells, killing up to 90% of them. Our results open an avenue for designing efficient drug delivery carriers compatible with a wide range of therapeutics.
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Affiliation(s)
- Nga T Ho
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- School of Natural Sciences, University of California, Merced, CA 93434
| | - Marc Siggel
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Karen V Camacho
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jacqueline M Hicks
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- Department of Regenerative Medicine and Cellular Therapies, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
- School of Natural Sciences, University of California, Merced, CA 93434
| | - Yuliang Zhang
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - 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 of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550;
- School of Natural Sciences, University of California, Merced, CA 93434
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13
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Omarova M, Zhang Y, Mkam Tsengam IK, He J, Yu T, Zhang D, John V. Hydrophobe Containing Polypeptoids Complex with Lipids and Induce Fusogenesis of Lipid Vesicles. J Phys Chem B 2021; 125:3145-3152. [PMID: 33730500 PMCID: PMC8041297 DOI: 10.1021/acs.jpcb.0c11477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/07/2021] [Indexed: 12/19/2022]
Abstract
The hydrophobic effect of alkyl group insertion into phospholipid bilayers is exploited in modifying and modulating vesicle structure. We show that amphiphilic polypeptoids (peptide mimics) with n-decyl side chains, which we term as hydrophobe-containing polypeptoids (HCPs), can insert the alkyl hydrophobes into the membrane bilayer of phospholipid-based vesicles. Such insertion leads to disruption of the liposomes and the formation of HCP-lipid complexes that are colloidally stable in aqueous solution. Interestingly, when these complexes are added to fresh liposomes, remnant uncomplexed hydrophobes (the n-decyl groups) bridge liposomes and fuse them. The fusion leads to the engulfing of liposomes and the formation of multilayered vesicles. The morphology of the liposome system can be changed from stopping fusion and forming clustered vesicles to the continued formation of multilayered liposomes simply by controlling the amount of the HCP-lipid complex added. The entire procedure occurs in aqueous systems without the addition of any other solvents. There are several implications to these observations including the biological relevance of mimicking fusogenic proteins such as the SNARE proteins and the development of new drug delivery technologies to impact delivery to cell organelles.
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Affiliation(s)
- Marzhana Omarova
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Yueheng Zhang
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor Kevin Mkam Tsengam
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jibao He
- Coordinated
Instrumentation Facility, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tianyi Yu
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Donghui Zhang
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Vijay John
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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14
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Risselada HJ, Grubmüller H. How proteins open fusion pores: insights from molecular simulations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:279-293. [PMID: 33340336 PMCID: PMC8071795 DOI: 10.1007/s00249-020-01484-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.
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Affiliation(s)
- H. Jelger Risselada
- Department of Theoretical Physics, Georg-August University of Göttingen, Göttingen, Germany
- Leiden University, Leiden Institute of Chemistry (LIC), Leiden, The Netherlands
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Theoretical and Computational Biophysics Department, Göttingen, Germany
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15
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Rogers JR, Geissler PL. Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes. J Phys Chem B 2020; 124:5884-5898. [DOI: 10.1021/acs.jpcb.0c04139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julia R. Rogers
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phillip L. Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Pang YT, Ge Z, Zhang B, Xiu P, Li Q, Wang Y. Pore formation induced by nanoparticles binding to a lipid membrane. NANOSCALE 2020; 12:7902-7913. [PMID: 32227042 DOI: 10.1039/c9nr10534d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanoparticles (NPs) enter a cell primarily via endocytosis, during which they are engulfed by the cell and reside in lipid vesicles named endosomes. Apart from when an endosome is pinched off the plasma membrane, structural integrity of its lipid membrane is usually well maintained. Under certain circumstances, however, such structural integrity can be considerably perturbed by a nanoparticle. For instance, recent experiments [Chu et al., Sci. Rep., 2014, 4, 4495] indicate that nanodiamonds with sharp corners can escape from an endosome by piercing its lipid membrane. Nonetheless, the energetics of this behavior and how it may be controlled by membrane adhesion and NP morphology remain unclear. In this work, we employ continuum modeling to investigate membrane pore formation induced by the spontaneous binding of a sharp nanoparticle. Based on two axial-symmetric NP models, we characterize the indispensable role played by curvature heterogeneity, membrane adhesion, and the sharpness as well as the size of a nanoparticle in 'breaking' a lipid membrane. Apart from revealing a general mechanism of NP binding-induced membrane pore formation, our results provide the reference for improving the endosomal escape of nanoparticles through manipulating their morphology, a direction that can be explored either independently or combined with existing strategies targeting NP surface chemistry.
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Affiliation(s)
- Yui Tik Pang
- Department of Physics, Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
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17
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F Brandner A, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Sci Rep 2019; 9:16450. [PMID: 31712588 PMCID: PMC6848203 DOI: 10.1038/s41598-019-52760-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/21/2019] [Indexed: 11/09/2022] Open
Abstract
In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.
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Affiliation(s)
- Astrid F Brandner
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Simone Melchionna
- ISC-CNR, Dipartimento di Fisica, Università Sapienza, P.le A. Moro 5, 00185, Rome, Italy.,Lexma Technology 1337 Massachusetts Avenue, Arlington, MA, 02476, USA
| | - Philippe Derreumaux
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France. .,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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18
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Lu T, Guo H. How the Membranes Fuse: From Spontaneous to Induced. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Teng Lu
- Beijing National Laboratory for Molecular SciencesJoint Laboratory of Polymer Sciences and MaterialsState Key Laboratory of Polymer Physics and ChemistryInstitute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular SciencesJoint Laboratory of Polymer Sciences and MaterialsState Key Laboratory of Polymer Physics and ChemistryInstitute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- Division of Polymer Science and MaterialsSchool of Chemical SciencesUniversity of Chinese Academy of Sciences Beijing 100049 China
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19
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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20
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Naz S, Wang M, Han Y, Hu B, Teng L, Zhou J, Zhang H, Chen J. Enzyme-responsive mesoporous silica nanoparticles for tumor cells and mitochondria multistage-targeted drug delivery. Int J Nanomedicine 2019; 14:2533-2542. [PMID: 31114189 PMCID: PMC6497824 DOI: 10.2147/ijn.s202210] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Drug delivery systems (DDS) capable of targeting both cell and organelle levels are highly desirable for effective cancer therapy. In this study, we developed a novel enzyme-responsive, multistage-targeted anticancer DDS based on mesoporous silica nanoparticles (MSNs), which possessed both CD44-targeting and mitochondrial-targeting properties. Materials and methods: Triphenylphosphine (TPP), a mitochondria-targeting compound, was grafted onto the surface of MSNs firstly. Then, Doxorubicin (Dox) was encapsulated into the pore of MSNs, followed by capping with tumor-targeting molecules hyaluronic acid (HA) through electrostatic interactions to form the final product consist of Dox loaded, TPP attached, HA capped mesoporous silica nanoparticles (MSN-DPH). Results: Our results suggested that MSN-DPH was preferentially taken up by cancer cells via CD44 receptor-mediated endocytosis. Moreover, MSN-DPH mainly accumulated in mitochondria owing to the mitochondrial-targeting ability of TPP. Degradation of HA by overexpressed HAase facilitated the release of Dox in cancer cells. Thus, MSN-DPH efficiently killed the cancer cells while exhibited much lower cytotoxicity to normal cells. Conclusion: This study demonstrates a promising multistage-targeted DDS for cancer chemotherapy.
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Affiliation(s)
- Safia Naz
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Mingyu Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Yuning Han
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Bin Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Liping Teng
- Wuxi School of Medicine, Jiangnan University, Wuxi, People’s Republic of China
| | - Juan Zhou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Huijie Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
| | - Jinghua Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, People’s Republic of China
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21
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Advances in materials for cellular applications (Review). Biointerphases 2019; 14:010801. [PMID: 30803241 DOI: 10.1116/1.5083803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The goal of this review is to highlight materials that show exciting promise for either entirely new cellular-level applications or new approaches to long-standing biological challenges. The authors start with two more established materials, graphene and carbon nanotubes, and then progress to conducting polymers, followed by an overview of the microresonators, nanowires, and spasers used as intracellular lasers. These materials provide new approaches to gene and drug delivery, cellular regeneration, mechanical sensing, imaging, and the modulation and recording of cellular activity. Of specific interest is the comparison of these materials with existing technologies, the method of cellular delivery, and the all-encompassing challenge of biocompatibility. Concluding remarks examine the extension of these materials from cellular-level experiments to in vivo applications, including the method of activation: light, electricity, and ultrasound. Overall, these materials and their associated applications illustrate the most recent advances in material-cell interactions.
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22
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Li Z, Zhang Y, Ma J, Meng Q, Fan J. Modeling Interactions between Liposomes and Hydrophobic Nanosheets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804992. [PMID: 30589212 DOI: 10.1002/smll.201804992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Indexed: 05/09/2023]
Abstract
2D nanomaterials could cause structural disruption and cytotoxic effects to cells, which greatly challenges their promising biomedical applications including biosensing, bioimaging, and drug delivery. Here, the physical and mechanical interaction between lipid liposomes and hydrophobic nanosheets is studied utilizing coarse-grained (CG) molecular dynamics (MD) simulations. The simulations reveal a variety of characteristic interaction morphologies that depend on the size and the orientation of nanosheets. Dynamic and thermodynamic analyses on the morphologic evolution provide insights into molecular motions such as "nanosheet rotation," "lipid extraction," "lipid flip-flop," and "lipid spreading." Driven by these molecular motions, hydrophobic nanosheets cause morphologic changes of liposomes. The lipid bilayer structure can be corrugated, and the overall liposome sphere can be split or collapsed by large nanosheets. In addition, nanosheets embedded into lipid bilayers greatly weaken the fluidity of lipids, and this effect can be cumulatively enhanced as nanosheets continuously intrude. These results could facilitate molecular-level understanding on the cytotoxicity of nanomaterials, and help future nanotoxicology studies associating computational modeling with experiments.
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Affiliation(s)
- Zhen Li
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Yonghui Zhang
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Jiale Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Qiangqiang Meng
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, 518057, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Hong Kong, China
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23
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Pérez-Luna V, Moreno-Aguilar C, Arauz-Lara JL, Aranda-Espinoza S, Quintana M. Interactions of Functionalized Multi-Wall Carbon Nanotubes with Giant Phospholipid Vesicles as Model Cellular Membrane System. Sci Rep 2018; 8:17998. [PMID: 30573758 PMCID: PMC6302088 DOI: 10.1038/s41598-018-36531-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 11/23/2018] [Indexed: 11/21/2022] Open
Abstract
Carbon Nanotubes (CNTs) are considered alternative materials for the design of advanced drug and gene delivery vectors. However, the mechanism responsible for the cellular membrane intake of CNTs is not well understood. In the present study, we show how multi-walled carbon nanotubes (MWCNTs) owning different surface properties, interact with giant unilamellar vesicles (GUVs), a simple model system for cellular membranes. In particular, we want to address the hydrophilic/hydrophobic interactions between MWCNTs and lipid membranes and the subsequent mechanical properties changes of the systems. In order to elucidate this interaction, we made the following chemical modifications on MWCNTs: oxidized MWCNTs (ox-MWCNTs) displaying reduced hydrophobic surface character, pristine MWCNTs (p-MWCNTs), and alkyl functionalized MWCNTs (alk-MWCNTs) exhibiting enhanced hydrophobic surface properties, were put in contact with GUVs and observed by confocal microscopy. Our observations revealed that the interaction between the CNTs and GUVs depends on the type of chemical functionalization: ox-MWCNTs remain at the membrane interacting with the polar head of the phospholipids, p-MWCNTs internalize GUVs spontaneously, and alk-MWCNTs persist inside the membrane. The mechanical properties of MWCNTs@GUVs systems were measured using the electrodeformation method, which shows an increased bending stiffness (κ) of the GUVs as MWCNTs concentration increases. High concentrations of p-MWCNTs and alk-MWCNTs induced vesicle adhesion; p-MWCNTs produced a considerable reduction in the average size of the GUVs, while alk-MWCNTs form complex stable structures inside the membrane. The statistical analyses of the experimental results are compared with available computer simulations. The picture emerging from our results is that the interaction between GUVs and MWCNTs is due mainly to hydrophobicity.
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Affiliation(s)
- Verónica Pérez-Luna
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, 78290, San Luis Potosí, SLP, Mexico
| | - Carlos Moreno-Aguilar
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, 78290, San Luis Potosí, SLP, Mexico
| | - José Luis Arauz-Lara
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, 78290, San Luis Potosí, SLP, Mexico
| | - Said Aranda-Espinoza
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, 78290, San Luis Potosí, SLP, Mexico.
| | - Mildred Quintana
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, 78290, San Luis Potosí, SLP, Mexico. .,Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av, Sierra Leona 550, 78210, San Luis Potosí, SLP, Mexico.
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24
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Sanborn JR, Chen X, Yao YC, Hammons JA, Tunuguntla RH, Zhang Y, Newcomb CC, Soltis JA, De Yoreo JJ, Van Buuren A, Parikh AN, Noy A. Carbon Nanotube Porins in Amphiphilic Block Copolymers as Fully Synthetic Mimics of Biological Membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1803355. [PMID: 30368926 DOI: 10.1002/adma.201803355] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Biological membranes provide a fascinating example of a separation system that is multifunctional, tunable, precise, and efficient. Biomimetic membranes, which mimic the architecture of cellular membranes, have the potential to deliver significant improvements in specificity and permeability. Here, a fully synthetic biomimetic membrane is reported that incorporates ultra-efficient 1.5 nm diameter carbon nanotube porin (CNTPs) channels in a block-copolymer matrix. It is demonstrated that CNTPs maintain high proton and water permeability in these membranes. CNTPs can also mimic the behavior of biological gap junctions by forming bridges between vesicular compartments that allow transport of small molecules.
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Affiliation(s)
- Jeremy R Sanborn
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- University of California Davis, Davis, CA, 95616, USA
| | - Xi Chen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Yun-Chiao Yao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Joshua A Hammons
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Ramya H Tunuguntla
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Yuliang Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Christina C Newcomb
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jennifer A Soltis
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Materials Science and Engineering and Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Anthony Van Buuren
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Atul N Parikh
- University of California Davis, Davis, CA, 95616, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
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25
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Palanikumar L, Kim J, Oh JY, Choi H, Park MH, Kim C, Ryu JH. Hyaluronic Acid-Modified Polymeric Gatekeepers on Biodegradable Mesoporous Silica Nanoparticles for Targeted Cancer Therapy. ACS Biomater Sci Eng 2018; 4:1716-1722. [DOI: 10.1021/acsbiomaterials.8b00218] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- L. Palanikumar
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jimin Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun Yong Oh
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Huyeon Choi
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Myoung-Hwan Park
- Department of Chemistry, Sahmyook University, Seoul 01795, Republic of Korea
| | - Chaekyu Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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26
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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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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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Dinda S, Mandal D, Sarkar S, Das PK. Self-Assembled Vesicle-Carbon Nanotube Conjugate Formation through a Boronate-Diol Covalent Linkage. Chemistry 2017; 23:15194-15202. [DOI: 10.1002/chem.201703452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Soumik Dinda
- Department of Biological Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700 032 India
| | - Deep Mandal
- Department of Biological Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700 032 India
| | - Saheli Sarkar
- Department of Biological Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700 032 India
| | - Prasanta Kumar Das
- Department of Biological Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700 032 India
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Xiong K, Zhao J, Yang D, Cheng Q, Wang J, Ji H. Cooperative wrapping of nanoparticles of various sizes and shapes by lipid membranes. SOFT MATTER 2017; 13:4644-4652. [PMID: 28650048 DOI: 10.1039/c7sm00345e] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Understanding the interaction between nanoparticles (NPs) and cell membranes is crucial for the design of NP-based drug delivery systems and for the assessment of the risks exerted by the NPs. Recent experimental and theoretical studies have shown that cell membranes can mediate attraction between NPs and form tubular structures to wrap multiple NPs. However, the cooperative wrapping process is still not well understood, and the shape effect of NPs is not considered. In this article, we use large-scale coarse-grained molecular dynamics (CGMD) simulations to study the cooperative wrapping of NPs when a varying number of NPs adhered to the membrane. Spherical, prolate and oblate NPs of different sizes are considered in this study. We find that, in addition to tubular structures, the membrane can form a pocket-like and a handle-like structure to wrap multiple NPs depending on the size and shape of the NPs. Furthermore, we find that NPs can mediate membrane hemifusion or fusion during this process. Our findings provide new insights into the interaction of NPs with the cell membrane.
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Affiliation(s)
- Kai Xiong
- Beijing Municipal Key Laboratory of Resource Environment and GIS, College of Resource Environment and Tourism, Capital Normal University, Beijing 100048, China
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