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Lee D, Lee J, Kim W, Suh Y, Park J, Kim S, Kim Y, Kwon S, Jeong S. Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308915. [PMID: 38932669 DOI: 10.1002/advs.202308915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.
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Affiliation(s)
- Dakyeon Lee
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jaekang Lee
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Woojin Kim
- Department of Materials Science and Engineering, Kookmin University, Seoul, 02707, Republic of Korea
| | - Yeongjoo Suh
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Jiwoo Park
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - YongJoo Kim
- Department of Materials Science and Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sunyoung Kwon
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
- Center for Artificial Intelligence Research, Pusan National University, Busan, 46241, Republic of Korea
| | - Sanghwa Jeong
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
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Lee Y, Kim W, Cho Y, Yoon M, Lee S, Lee J, Oh S, Song Y, Lee BJ, Kim Y, Cho SY. Rational Design of 3D Polymer Corona Interfaces of Single-Walled Carbon Nanotubes for Receptor-Free Virus Recognition. ACS NANO 2024; 18:13214-13225. [PMID: 38717114 DOI: 10.1021/acsnano.4c02130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Facing the escalating threat of viruses worldwide, the development of efficient sensor elements for rapid virus detection has never been more critical. Traditional point-of-care (POC) sensors struggle due to their reliance on fragile biological receptors and limited adaptability to viral strains. In this study, we introduce a nanosensor design for receptor-free virus recognitions using near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) functionalized with a poly(ethylene glycol) (PEG)-phospholipid (PEG-lipid) array. Three-dimensional (3D) corona interfaces of the nanosensor array enable selective and sensitive detection of diverse viruses, including Ebola, Lassa, H3N2, H1N1, Middle East respiratory syndrome (MERS), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), and SARS-CoV-2, even without any biological receptors. The PEG-lipid components, designed considering chain length, fatty acid saturation, molecular weight, and end-group moieties, allow for precise quantification of viral recognition abilities. High-throughput automated screening of the array demonstrates how the physicochemical properties of the PEG-lipid/SWCNT 3D corona interfaces correlate with viral detection efficiency. Utilizing molecular dynamics and AutoDock simulations, we investigated the impact of PEG-lipid components on 3D corona interface formation, such as surface coverage and hydrodynamic radius and specific molecular interactions based on chemical potentials. Our findings not only enhance detection specificity across various antigens but also accelerate the development of sensor materials for promptly identifying and responding to emerging antigen threats.
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Affiliation(s)
- Yullim Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Woojin Kim
- Department of Materials Science and Engineering, Kookmin University, Seoul 02707, Republic of Korea
| | - Youngwook Cho
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Minyeong Yoon
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seungju Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jungwoo Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sangyeon Oh
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yeongjun Song
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Brian J Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - YongJoo Kim
- Department of Materials Science and Engineering, Kookmin University, Seoul 02707, Republic of Korea
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Soo-Yeon Cho
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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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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4
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Almeida ER, Goliatt PVZC, Dos Santos HF, Picaud F. Modeling the Cellular Uptake of Functionalized Carbon Nanohorns Loaded with Cisplatin through a Breast Cancer Cell Membrane. Mol Pharm 2024; 21:38-52. [PMID: 37646561 DOI: 10.1021/acs.molpharmaceut.3c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The cisplatin encapsulation into carbon nanohorns (CNH) is a promising nanoformulation to circumvent the drug dissipation and to specifically accumulate it in tumor sites. Herein, biased molecular dynamics simulations were used to analyze the transmembrane transport of the CNH loaded with cisplatin through a breast cancer cell membrane prototype. The simulations revealed a four-stage mechanism: approach, insertion, permeation, and internalization. Despite the lowest structural disturbance of the membrane provided by the nanocarrier, the average free energy barrier for the translocation was 55.2 kcal mol-1, suggesting that the passive process is kinetically unfavorable. In contrast, the free energy profiles revealed potential wells of -6.8 kcal mol-1 along the insertion stage in the polar heads region of the membrane, which might enhance the retention of the drug in tumor sites; therefore, the most likely cisplatin delivery mechanism should involve the adsorption and retention of CNH on the surface of cancer cells, allowing the loaded cisplatin be slowly released and passively transported through the cell membrane.
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Affiliation(s)
- Eduardo R Almeida
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, Minas Gerais 36036-330, Brazil
- Laboratoire de Nanomédecine, Imagerie et Thérapeutiques, EA 4662, Centre Hospitalier Universitaire de Besançon, Université de Franche-Comté, 16 route de Gray, 25030 Besançon, Cedex, France
| | - Priscila V Z Capriles Goliatt
- Grupo de Modelagem Computacional Aplicada (GMCA), Programa de Pós-Graduação em Modelagem Computacional (PGMC), Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, Minas Gerais 36036-330, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, Minas Gerais 36036-330, Brazil
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutiques, EA 4662, Centre Hospitalier Universitaire de Besançon, Université de Franche-Comté, 16 route de Gray, 25030 Besançon, Cedex, France
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Gul G, Faller R, Ileri-Ercan N. Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers. Biophys J 2023; 122:1748-1761. [PMID: 37056052 PMCID: PMC10209035 DOI: 10.1016/j.bpj.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
In the present work, we describe Martini3 coarse-grained models of polystyrene and carboxyl-terminated polystyrene functionalized carbon nanotubes (CNTs) and investigate their interactions with lipid bilayers with and without cholesterol (CHOL) using molecular dynamics simulations. By changing the polystyrene chain length and grafting density at the end ring of the CNTs at two different nanotube concentrations, we observe the translocation of nanoparticles as well as changes in the lipid bilayer properties. Our results show that all developed models passively diffuse into the membranes without causing any damage to the membrane integrity, although high concentrations of CNTs induce structural and elastic changes in lipid bilayers. In the presence of CHOL, increasing CNT concentration results in decreased rates of CHOL transmembrane motions. On the other hand, CNTs are prone to lipid and polystyrene blockage, which affects their equilibrated configurations, and tilting behavior within the membranes. Hence, we demonstrate that polystyrene-functionalized CNTs are promising drug-carrier agents. However, polystyrene chain length and grafting density are important factors to consider to enhance the efficiency of drug delivery.
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Affiliation(s)
- Gulsah Gul
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey; Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Roland Faller
- Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Nazar Ileri-Ercan
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.
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6
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Singh RP, Kaur T. HRMAS-NMR and simulation study of the self-assembly of surfactants on carbon nanotubes. Phys Chem Chem Phys 2023; 25:12900-12913. [PMID: 37165884 DOI: 10.1039/d2cp03762a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Polyethoxylated surfactants, such as those of the Tween and Pluronic series, are commonly used to disperse carbon nanotubes (CNTs) and other nanoparticles. However, the current understanding of the nature of interactions between these surfactants and CNTs is limited. The nature of the interactions between surfactants (Tween-80 [T80] and Pluronic F68 [PF68]) and CNTs was investigated using high-resolution magic angle spinning nuclear magnetic resonance (HRMAS-NMR) and coarse-grained molecular dynamics (MD) simulations. HRMAS-NMR revealed that T80 molecules interact with single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) via the oleyl chain, whereas PF68 molecules interact with the surface of SWCNTs and MWCNTs via the polypropylene oxide residues. The polyethylene oxide chains were oriented towards the external aqueous environment. The HRMAS-NMR results were supported by MD simulations, and the latter provided further insights into the nature of the interactions.
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Affiliation(s)
- Raman Preet Singh
- Department of Pharmaceutical Sciences, Government Polytechnic College for Girls, Patiala, PB, 147 001, India.
| | - Taranpreet Kaur
- Department of Biotechnology, Government Mohindra College, Patiala, PB, 147 001, India
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Zhang S, Hettige JJ, Li Y, Jian T, Yang W, Yao YC, Zheng R, Lin Z, Tao J, De Yoreo JJ, Baer M, Noy A, Chen CL. Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206810. [PMID: 36811318 DOI: 10.1002/smll.202206810] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/06/2023] [Indexed: 05/25/2023]
Abstract
Robust and cost-effective membrane-based separations are essential to solving many global crises, such as the lack of clean water. Even though the current polymer-based membranes are widely used for separations, their performance and precision can be enhanced by using a biomimetic membrane architecture that consists of highly permeable and selective channels embedded in a universal membrane matrix. Researchers have shown that artificial water and ion channels, such as carbon nanotube porins (CNTPs), embedded in lipid membranes can deliver strong separation performance. However, their applications are limited by the relative fragility and low stability of the lipid matrix. In this work, we demonstrate that CNTPs can co-assemble into two dimension (2D) peptoid membrane nanosheets, opening up a way to produce highly programmable synthetic membranes with superior crystallinity and robustness. A combination of molecular dynamics (MD) simulations, Raman spectroscopy, X-ray diffraction (XRD), and atomic force microscopy (AFM) measurements to verify the co-assembly of CNTP and peptoids are used and show that it does not disrupt peptoid monomer packing within the membrane. These results provide a new option for designing affordable artificial membranes and highly robust nanoporous solids.
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Affiliation(s)
- Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Jeevapani J Hettige
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yuhao Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, 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
| | - Renyu Zheng
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Zhixing Lin
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Jinhui Tao
- 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
- Materials Science and Engineering, University of Washington, Seattle, WA, 98105, USA
| | - Marcel Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, 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
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98105, USA
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Isci R, Baysak E, Kesan G, Minofar B, Eroglu MS, Duygulu O, Gorkem SF, Ozturk T. Non-covalent modification of single wall carbon nanotubes (SWCNTs) by thienothiophene derivatives. NANOSCALE 2022; 14:16602-16610. [PMID: 36317494 DOI: 10.1039/d2nr04582f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Non-covalent functionalization of single wall carbon nanotubes (SWCNTs) has been conducted using several binding agents with surface π-interaction forces in recent studies. Herein, we present the first example of non-covalent functionalization of sidewalls of SWCNTs using thienothiophene (TT) derivatives without requiring any binding agents. Synthesized TT derivatives, TT-CN-TPA, TT-CN-TPA2 and TT-COOH-TPA, were attached directly to SWCNTs through non-covalent interactions to obtain new TT-based SWCNT hybrids, HYBRID 1-3. Taking advantage of the presence of sulfur atoms in the structure of TT, HYBRID 1, as a representative, was treated with Au nanoparticles for the adsorption of Au by sulfur atoms, which generated clear TEM images of the particles. The images indicated the attachment of TTs to the surface of SWCNTs. Thus, the presence of sulfur atoms in TT units made the binding of TTs to SWCNTs observable via TEM analysis through adsorption of Au nanoparticles by the sulfur atoms. Surface interactions between TTs and SWCNTs of the new hybrids were also clarified by classical molecular dynamic simulations, a quantum mechanical study, and SEM, TEM, AFM and contact angle (CA) analyses. The minimum distance between a TT and a SWCNT reached up to 3.5 Å, identified with strong peaks on a radial distribution function (RDF), while maximum interaction energies were raised to -316.89 kcal mol-1, which were determined using density functional theory (DFT).
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Affiliation(s)
- Recep Isci
- Department of Chemistry, Science Faculty, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
| | - Elif Baysak
- Department of Chemistry, Science Faculty, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
| | - Gurkan Kesan
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská, 1760, 370 05, České Budějovice, Czech Republic
| | - Babak Minofar
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská, 1760, 370 05, České Budějovice, Czech Republic
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Mehmet S Eroglu
- Metallurgical and Materials Engineering Dept., Faculty of Engineering, Marmara University, Aydınevler, Maltepe, 34854, Istanbul, Turkey
- Chemistry Group, Organic Chemistry Laboratory, TUBITAK National Metrology Institute, Gebze, Kocaeli, 54 41470, Turkey
| | - Ozgur Duygulu
- Material Technologies, TUBITAK Marmara Research Center, Gebze, Kocaeli, 41470, Turkey
| | - Sultan F Gorkem
- Chemistry Department, Eskisehir Technical University, 26470 Eskisehir, Turkey
| | - Turan Ozturk
- Department of Chemistry, Science Faculty, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
- Chemistry Group, Organic Chemistry Laboratory, TUBITAK National Metrology Institute, Gebze, Kocaeli, 54 41470, Turkey
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Gul G, Faller R, Ileri-Ercan N. Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery. Biophys J 2022; 121:4271-4279. [PMID: 36230001 PMCID: PMC9703093 DOI: 10.1016/j.bpj.2022.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/28/2022] [Accepted: 10/11/2022] [Indexed: 12/14/2022] Open
Abstract
To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.
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Affiliation(s)
- Gulsah Gul
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey; Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Roland Faller
- Department of Chemical Engineering, University of California, Davis, Davis, California
| | - Nazar Ileri-Ercan
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey.
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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: 123] [Impact Index Per Article: 61.5] [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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12
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Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria. Nat Commun 2022; 13:2417. [PMID: 35577779 PMCID: PMC9110379 DOI: 10.1038/s41467-022-30185-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/20/2022] [Indexed: 11/15/2022] Open
Abstract
The delivery of genetic material into plants has been historically challenging due to the cell wall barrier, which blocks the passage of many biomolecules. Carbon nanotube-based delivery has emerged as a promising solution to this problem and has been shown to effectively deliver DNA and RNA into intact plants. Mitochondria are important targets due to their influence on agronomic traits, but delivery into this organelle has been limited to low efficiencies, restricting their potential in genetic engineering. This work describes the use of a carbon nanotube-polymer hybrid modified with functional peptides to deliver DNA into intact plant mitochondria with almost 30 times higher efficiency than existing methods. Genetic integration of a folate pathway gene in the mitochondria displays enhanced plant growth rates, suggesting its applications in metabolic engineering and the establishment of stable transformation in mitochondrial genomes. Furthermore, the flexibility of the polymer layer will also allow for the conjugation of other peptides and cargo targeting other organelles for broad applications in plant bioengineering. The delivery of genetic material into plants is challenging due to the cell wall barrier. Here, the authors hybridize polymer-coated carbon nanotubes with functional peptides to deliver plasmid DNA cargo into intact plant mitochondria for transient expression and homologous recombination at high efficiency.
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13
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401,;
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,;
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14
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Umbrella Sampling Simulations of Carbon Nanoparticles Crossing Immiscible Solvents. Molecules 2022; 27:molecules27030956. [PMID: 35164220 PMCID: PMC8837927 DOI: 10.3390/molecules27030956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
We use molecular dynamics to compute the free energy of carbon nanoparticles crossing a hydrophobic–hydrophilic interface. The simulations are performed on a biphasic system consisting of immiscible solvents (i.e., cyclohexane and water). We solvate a carbon nanoparticle into the cyclohexane layer and use a pull force to drive the nanoparticle into water, passing over the interface. Next, we accumulate a series of umbrella sampling simulations along the path of the nanoparticle and compute the solvation free energy with respect to the two solvents. We apply the method on three carbon nanoparticles (i.e., a carbon nanocone, a nanotube, and a graphene nanosheet). In addition, we record the water-accessible surface area of the nanoparticles during the umbrella simulations. Although we detect complete wetting of the external surface of the nanoparticles, the internal surface of the nanotube becomes partially wet, whereas that of the nanocone remains dry. This is due to the nanoconfinement of the particular nanoparticles, which shields the hydrophobic interactions encountered inside the pores. We show that cyclohexane molecules remain attached on the concave surface of the nanotube or the nanocone without being disturbed by the water molecules entering the cavity.
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15
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Barden DR, Vashisth H. Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes. Front Chem 2021; 9:753635. [PMID: 34778209 PMCID: PMC8586425 DOI: 10.3389/fchem.2021.753635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide-appended Pillar[5]arene (PAP) is an artificial water channel that can be incorporated into lipid and polymeric membranes to achieve high permeability and enhanced selectivity for angstrom-scale separations [Shen et al. Nat. Commun.9:2294 (2018)]. In comparison to commonly studied rigid carbon nanotubes, PAP channels are conformationally flexible, yet these channels allow a high water permeability [Y. Liu and H. Vashisth Phys. Chem. Chem. Phys.21:22711 (2019)]. Using molecular dynamics (MD) simulations, we study water dynamics in PAP channels embedded in biological (lipid) and biomimetic (block-copolymer) membranes to probe the effect of the membrane environment on water transport characteristics of PAP channels. We have resolved the free energy surface and local minima for water diffusion within the channel in each type of membrane. We find that water follows single file transport with low free-energy barriers in regions surroundings the central ring of the PAP channel and the single file diffusivity of water correlates with the number of hydrogen bonding sites within the channel, as is known for other sub-nm pore-size synthetic and biological water channels [Horner et al. Sci. Adv.1:e1400083 (2015)].
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Affiliation(s)
- Daniel Ryan Barden
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, United States
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16
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Ebrahimi M, Foroutan M. High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels. J Phys Chem B 2021; 125:11566-11581. [PMID: 34615355 DOI: 10.1021/acs.jpcb.1c04507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10-13 cm3·s-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.
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Affiliation(s)
- Mina Ebrahimi
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
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17
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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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18
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Robinson F, Park C, Kim M, Kim D. Defect induced deformation effect on water transport through (6, 6) carbon nanotube. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Dettmann LF, Kühn O, Ahmed AA. Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution. RSC Adv 2021; 11:27734-27744. [PMID: 35480645 PMCID: PMC9037801 DOI: 10.1039/d1ra04439g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/06/2021] [Indexed: 01/02/2023] Open
Abstract
Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater. The binding mechanisms of nanoplastics (NPs) to carbon nanotubes as hydrophobic environmental systems have been explored by coarse-grained MD simulations. The results could be closely connected to fate of NPs in soil and water treatment technologies.![]()
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Affiliation(s)
- Lorenz F Dettmann
- University of Rostock, Institute of Physics Albert-Einstein-Str. 23-24 D-18059 Rostock Germany
| | - Oliver Kühn
- University of Rostock, Institute of Physics Albert-Einstein-Str. 23-24 D-18059 Rostock Germany .,University of Rostock, Department of Life, Light and Matter (LLM) Albert-Einstein-Str. 25 D-18059 Rostock Germany
| | - Ashour A Ahmed
- University of Rostock, Institute of Physics Albert-Einstein-Str. 23-24 D-18059 Rostock Germany .,University of Rostock, Department of Life, Light and Matter (LLM) Albert-Einstein-Str. 25 D-18059 Rostock Germany
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20
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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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21
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Haridasan N, Sathian SP. Rotational dynamics of proteins in nanochannels: role of solvent's local viscosity. NANOTECHNOLOGY 2021; 32:225102. [PMID: 33621966 DOI: 10.1088/1361-6528/abe906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Viscosity variation of solvent in local regions near a solid surface, be it a biological surface of a protein or an engineered surface of a nanoconfinement, is a direct consequence of intermolecular interactions between the solid body and the solvent. The current coarse-grained molecular dynamics study takes advantage of this phenomenon to investigate the anomaly in a solvated protein's rotational dynamics confined using a representative solid matrix. The concept of persistence time, the characteristic time of structural reordering in liquids, is used to compute the solvent's local viscosity. With an increase in the degree of confinement, the confining matrix significantly influences the solvent molecule's local viscosity present in the protein hydration layer through intermolecular interactions. This effect contributes to the enhanced drag force on protein motion, causing a reduction in the rotational diffusion coefficient. Simulation results suggest that the direct matrix-protein non-bonded interaction is responsible for the occasional jump and discontinuity in orientational motion when the protein is in very tight confinement.
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Affiliation(s)
- Navaneeth Haridasan
- Micro and Nanoscale Transport Lab, Applied Mechanics Department, Indian Institute of Technology Madras, Chennai, India
| | - Sarith P Sathian
- Micro and Nanoscale Transport Lab, Applied Mechanics Department, Indian Institute of Technology Madras, Chennai, India
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22
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Gotzias A. Binding Free Energy Calculations of Bilayer Graphenes Using Molecular Dynamics. J Chem Inf Model 2021; 61:1164-1171. [PMID: 33663215 DOI: 10.1021/acs.jcim.1c00043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bilayer graphenes are dimeric assemblies of single graphene layers bound together by π-complexation interactions. Controlling these assemblies can be complicated, as the layered compounds disperse in solvents or aggregate into higher columnar configurations and clusters. One way to assess the interactions that contribute to the stability of the layered compounds is to use molecular simulation. We perform pulling molecular dynamics on bilayer graphenes with different sizes and obtain the normal and shear force profiles of dissociation. We generate pathways of dissociation along the two directions and calculate the binding free energies of the structures with umbrella sampling simulations. We show that the dissociation process is direction-dependent. Along the shear direction, we compute the same free energy for the different samples, which validates the consistency of our simulations. We notice that the dissociation is less adiabatic on the normal than the shear direction, having an entropic contribution to the Gibbs energy. This contribution is more enhanced for the larger bilayer graphenes.
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Affiliation(s)
- Anastasios Gotzias
- Institute of Nanoscience and Nanotechnology, National Centre of Scientific Research Demokritos, 15310 Agia Paraskevi, Athens, Greece
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23
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Patel S, Srivastav AK, Gupta SK, Kumar U, Mahapatra SK, Gajjar PN, Banerjee I. Carbon nanotubes for rapid capturing of SARS-COV-2 virus: revealing a mechanistic aspect of binding based on computational studies. RSC Adv 2021; 11:5785-5800. [PMID: 35423109 PMCID: PMC8694767 DOI: 10.1039/d0ra08888a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e.6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of -87.09 kcal mol-1 with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits.
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Affiliation(s)
- Shivkumar Patel
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | | | - Sanjeev K Gupta
- Computational Materials and Nanoscience Group, Department of Physics, St. Xavier's College Ahmedabad 380009 India
| | - Umesh Kumar
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | - S K Mahapatra
- Department of Physics, Central University of Punjab Bathinda 151001 India
| | - P N Gajjar
- Department of Physics, University School of Sciences, Gujarat University Ahmedabad 380009 India
| | - I Banerjee
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
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24
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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25
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Sullivan K, Zhang Y, Lopez J, Lowe M, Noy A. Carbon nanotube porin diffusion in mixed composition supported lipid bilayers. Sci Rep 2020; 10:11908. [PMID: 32681044 PMCID: PMC7368039 DOI: 10.1038/s41598-020-68059-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/11/2020] [Indexed: 11/30/2022] Open
Abstract
Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.
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Affiliation(s)
- Kylee Sullivan
- Physics Department, Loyola University Maryland, Baltimore, MD, 21210, USA
| | - Yuliang Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Joseph Lopez
- Physics Department, Loyola University Maryland, Baltimore, MD, 21210, USA
| | - Mary Lowe
- Physics Department, Loyola University Maryland, Baltimore, MD, 21210, 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, 94343, USA.
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26
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Hammons JA, Ingólfsson HI, Lee JRI, Carpenter TS, Sanborn J, Tunuguntla R, Yao YC, Weiss TM, Noy A, Van Buuren T. Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles. NANOSCALE 2020; 12:6545-6555. [PMID: 32159198 DOI: 10.1039/c9nr09973e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bilayer vesicles that mimic a real biological cell can be tailored to carry out a specific function by manipulating the molecular composition of the amphiphiles. These bio-inspired and bio-mimetic structures are increasingly being employed for a number of applications from drug delivery to water purification and beyond. Complex hybrid bilayers are the key building blocks for fully synthetic vesicles that can mimic biological cell membranes, which often contain a wide variety of molecular species. While the assembly and morpholgy of pure phospholid bilayer vesicles is well understood, the functionality and structure dramaticlly changes when copolymer and/or carbon nanotube porins (CNTP) are added. The aim of this study is to understand how the collective molecular interactions within hybrid vesicles affect their nanoscale structure and properties. In situ small and wide angle X-ray scattering (SAXS/WAXS) and molecular dynamics simulations (MD) are used to investigate the morphological effect of molecular interactions between polybutadiene polyethylene oxide, lipids and carbon nanotubes (CNT) within the hybrid vesicle bilayer. Within the lipid/copolymer system, the hybrid bilayer morphology transitions from phase separated lipid and compressed copolymer at low copolymer loadings to a mixed bilayer where opposing lipids are mostly separated from the inner region. This transition begins between 60 wt% and 70 wt%, with full homogenization observed by 80 wt% copolymer. The incorporation of CNT into the hybrid vesicles increases the bilayer thickness and enhances the bilayer symmetry. Analysis of the WAXS and MD indicate that the CNT-dioleoyl interactions are much stronger than the CNT-polybutadiene.
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Affiliation(s)
- Joshua A Hammons
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, USA.
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27
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Guo Y, Werner M, Fleury JB, Baulin VA. Unexpected Cholesterol-Induced Destabilization of Lipid Membranes near Transmembrane Carbon Nanotubes. PHYSICAL REVIEW LETTERS 2020; 124:038001. [PMID: 32031854 DOI: 10.1103/physrevlett.124.038001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Cholesterol is a crucial component of mammalian cell membranes that takes part in many vital processes. It is generally accepted that cholesterol stabilizes the membrane and induces transitions into ordered states. In contrast to expectations, we demonstrate that cholesterol can destabilize the membrane by creating a nanodomain around a perpendicularly embedded ultrashort carbon nanotube (CNT), and we show that cholesterol triggers the translocation of an ultrashort CNT through the cell membrane. Using atomistic simulations, we report the existence of a nanoscale domain around an ultrashort carbon nanotube within a crossover distance of 0.9 nm from the surface of the nanotube, where the properties of the bilayer are different from the bulk: the domain is characterized by increased fluctuations, increased thickness, and increased order of the lipids with respect to the bulk. Cholesterol decreases the thickness and order of lipids and increases the fluctuations with respect to a pure lipid bilayer. Experimentally, we confirm that cholesterol nanodomains provoke spontaneous translocation of nanotubes through a lipid bilayer even for low membrane tensions. A specially designed microfluidic device allows us to trace the kinetic pathway of the translocation process and establish the threshold cholesterol concentration of 20% for translocation. The reported nanoscale cholesterol-induced membrane restructuring near the ultrashort CNT in lipid membranes enables precise control and specific targeting of a membrane using cholesterol. As an example, it may allow for specific targeting between cholesterol-rich mammalian cells and cholesterol-poor bacterial cells.
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Affiliation(s)
- Yachong Guo
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Marco Werner
- Leibniz-Institut für Polymerforschung Dresden, Hohe Strasse 6, 01069 Dresden, Germany
| | - Jean Baptiste Fleury
- Universitat des Saarlandes, Experimental Physics and Center for Biophysics, 66123 Saarbruecken, Germany
| | - Vladimir A Baulin
- Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, 26 Avinguda dels Paisos Catalans, 43007 Tarragona, Spain
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28
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Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G. High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Res 2020; 48:924-933. [PMID: 31777925 PMCID: PMC6954412 DOI: 10.1093/nar/gkz1096] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 12/25/2022] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
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Affiliation(s)
- Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Grace Thierolf
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 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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29
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Liu Y, Vashisth H. Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes. Phys Chem Chem Phys 2019; 21:22711-22721. [PMID: 31454001 DOI: 10.1039/c9cp04408f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide appended pillar[5]arene (PAP) is an artificial water channel resembling biological water channel proteins, which has shown a significant potential for designing bioinspired water purification systems. Given that PAP channels need to be incorporated at a high density in membrane matrices, it is critical to examine the role of channel-channel and channel-membrane interactions in governing the structural and functional characteristics of channels. To resolve the atomic-scale details of these interactions, we have carried out atomistic molecular dynamics (MD) simulations of multiple PAP channels inserted in a lipid or a block-copolymer (BCP) membrane matrix. Classical MD simulations on a sub-microsecond timescale showed clustering of channels only in the lipid membrane, but enhanced sampling MD simulations showed thermodynamically-favorable dimerized states of channels in both lipid and BCP membranes. The dimerized configurations of channels, with an extensive buried surface area, were stabilized via interactions between the aromatic groups in the peptide arms of neighboring channels. The conformational metrics characterizing the orientational and structural changes in channels revealed a higher flexibility in the lipid membrane as opposed to the BCP membrane although hydrogen bonds between the channel and the membrane molecules were not a major contributor to the stability of channels in the BCP membrane. We also found that the channels undergo wetting/dewetting transitions in both lipid and BCP membranes with a marginally higher probability of undergoing a dewetting transition in the BCP membrane. Collectively, these results highlight the role of channel dynamics in governing channel-channel and channel-membrane interfacial interactions, and provide atomic-scale insights needed to design stable and functional biomimetic membranes for efficient separations.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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30
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Abstract
We employed molecular dynamics simulations on the water solvation of conically shaped carbon nanoparticles. We explored the hydrophobic behaviour of the nanoparticles and investigated microscopically the cavitation of water in a conical confinement with different angles. We performed additional molecular dynamics simulations in which the carbon structures do not interact with water as if they were in vacuum. We detected a waving on the surface of the cones that resembles the shape agitations of artificial water channels and biological porins. The surface waves were induced by the pentagonal carbon rings (in an otherwise hexagonal network of carbon rings) concentrated near the apex of the cones. The waves were affected by the curvature gradients on the surface. They were almost undetected for the case of an armchair nanotube. Understanding such nanoscale phenomena is the key to better designed molecular models for membrane systems and nanodevices for energy applications and separation.
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31
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Feng X, Ma T, Yamaura D, Tadaki D, Hirano-Iwata A. Formation and Characterization of Air-Stable Lipid Bilayer Membranes Incorporated with Phthalocyanine Molecules. J Phys Chem B 2019; 123:6515-6520. [PMID: 31280566 DOI: 10.1021/acs.jpcb.9b05135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bilayer lipid membranes (BLMs) are used as basic frameworks for biosensors and biohybrid devices due to their unique properties, which include ultrathin thickness, ultrahigh resistivity, and self-assembling ability. However, BLMs can only form and maintain their structure in aqueous environments, which pose significant limitations to their use. In this work, we report on the formation of highly uniform hybrid BLMs at a water/air interface through self-assembly by simply doping the BLMs with a functional organic molecule, copper(II) 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (CuPc). By transferring the membrane onto substrates, we were able to produce stable hybrid BLMs under anhydrous conditions. Atomic force microscopy and X-ray diffraction measurements confirmed that the hybrid membranes were composed of single, highly uniform BLMs or stacks of BLMs. Fluorescence resonance energy transfer measurements indicated that the CuPc molecules were located between the hydrophobic tails of lipid molecules, forming a sandwich structure in the hybrid membranes. The hybrid BLMs fabricated by this method substantially expand the range of applications of BLMs to solid-state devices.
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32
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Vögele M, Köfinger J, Hummer G. Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. J Phys Chem B 2019; 123:5099-5106. [PMID: 31132280 PMCID: PMC6750896 DOI: 10.1021/acs.jpcb.9b01656] [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] [Indexed: 12/16/2022]
Abstract
![]()
We investigate
system-size effects on the rotational diffusion of membrane proteins
and other membrane-embedded molecules in molecular dynamics simulations. We find that
the rotational diffusion coefficient slows down relative to the infinite-system
value by a factor of one minus the ratio of protein and box areas.
This correction factor follows from the hydrodynamics of rotational
flows under periodic boundary conditions and is rationalized in terms
of Taylor–Couette flow. For membrane proteins like transporters,
channels, or receptors in typical simulation setups, the protein-covered
area tends to be relatively large, requiring a significant finite-size
correction. Molecular dynamics simulations of the protein adenine
nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid
membranes show that the hydrodynamic finite-size correction for rotational
diffusion is accurate in standard-use cases. The dependence of the
rotational diffusion on box size can be used to determine the membrane
viscosity.
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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 , 60438 Frankfurt am Main , Germany
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33
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Abstract
Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO2 transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.
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Affiliation(s)
- Christof Hannesschlaeger
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Andreas Horner
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Peter Pohl
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
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34
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Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G. Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. J Phys Chem B 2018; 122:11626-11639. [PMID: 30285443 DOI: 10.1021/acs.jpcb.8b07537] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We combine single-molecule Förster resonance energy transfer (single-molecule FRET) experiments with extensive all-atom molecular dynamics (MD) simulations (>100 μs) to characterize the conformational ensembles of single-stranded (ss) DNA and RNA in solution. From MD simulations with explicit dyes attached to single-stranded nucleic acids via flexible linkers, we calculate FRET efficiencies and fluorescence anisotropy decays. We find that dispersion-corrected water models alleviate the problem of overly abundant interactions between fluorescent dyes and the aromatic ring systems of nucleobases. To model dye motions in a computationally efficient and conformationally exhaustive manner, we introduce a dye-conformer library, built from simulations of dinucleotides with covalently attached dye molecules. We use this library to calculate FRET efficiencies for dT19, dA19, and rA19 simulated without explicit labels over a wide range of salt concentrations. For end-labeled homopolymeric pyrimidine ssDNA, MD simulations with the parmBSC1 force field capture the overall trend in salt-dependence of single-molecule FRET based distance measurements. For homopolymeric purine ssRNA and ssDNA, the DESRES and parmBSC1 force fields, respectively, provide useful starting points, even though our comparison also identifies clear deviations from experiment.
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Affiliation(s)
- Kara K Grotz
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , 60438 Frankfurt am Main , Germany
| | - Mark F Nueesch
- Department of Biochemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Erik D Holmstrom
- Department of Biochemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Marcel Heinz
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , 60438 Frankfurt am Main , Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , 60438 Frankfurt am Main , Germany
| | - Benjamin Schuler
- Department of Biochemistry , University of Zurich , 8057 Zurich , Switzerland.,Department of Physics , University of Zurich , 8057 Zurich , Switzerland
| | - 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
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35
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Biomimetic Membranes as a Technology Platform: Challenges and Opportunities. MEMBRANES 2018; 8:membranes8030044. [PMID: 30018213 PMCID: PMC6161077 DOI: 10.3390/membranes8030044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023]
Abstract
Biomimetic membranes are attracting increased attention due to the huge potential of using biological functional components and processes as an inspirational basis for technology development. Indeed, this has led to several new membrane designs and applications. However, there are still a number of issues which need attention. Here, I will discuss three examples of biomimetic membrane developments within the areas of water treatment, energy conversion, and biomedicine with a focus on challenges and applicability. While the water treatment area has witnessed some progress in developing biomimetic membranes of which some are now commercially available, other areas are still far from being translated into technology. For energy conversion, there has been much focus on using bacteriorhodopsin proteins, but energy densities have so far not reached sufficient levels to be competitive with state-of-the-art photovoltaic cells. For biomedical (e.g., drug delivery) applications the research focus has been on the mechanism of action, and much less on the delivery 'per se'. Thus, in order for these areas to move forward, we need to address some hard questions: is bacteriorhodopsin really the optimal light harvester to be used in energy conversion? And how do we ensure that biomedical nano-carriers covered with biomimetic membrane material ever reach their target cells/tissue in sufficient quantities? In addition to these area-specific questions the general issue of production cost and scalability must also be treated in order to ensure efficient translation of biomimetic membrane concepts into reality.
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36
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Abstract
Developing bioinspired artificial water channels may lead to the next-generation filtration membranes with ultra-high pore density and exclusive water permeability.
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Affiliation(s)
- Bing Gong
- Department of Chemistry
- University at Buffalo
- The State University of New York
- Buffalo
- USA
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