1
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Du Y, Luo Y, Gu Z. Molecular dynamics simulations reveal concentration-dependent blockage of graphene quantum dots to water channel protein openings. Sci Rep 2024; 14:26485. [PMID: 39489799 PMCID: PMC11532551 DOI: 10.1038/s41598-024-77592-3] [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: 08/06/2024] [Accepted: 10/23/2024] [Indexed: 11/05/2024] Open
Abstract
Graphene quantum dots (GQDs) have attracted significant attention across various scientific research areas due to their exceptional properties. However, studies on the potential toxicity of GQDs have yielded conflicting results. Therefore, a comprehensive evaluation of the toxicity profile of GQDs is essential for a thorough understanding of their biosafety. In this work, employing a molecular dynamics (MD) simulation approach, we investigate the interactions between GQDs and graphene oxide quantum dots (GOQDs) with the AQP1 water channel protein, aiming to explore the potential biological influence of GQDs/GOQDs. Our MD simulation results reveal that GQDs can adsorb to the loop region around the openings of AQP1 water channels, resulting in the blockage of these channels and potential toxicity. Interestingly, this blockage is concentration-dependent, with higher GQD concentrations leading to a greater likelihood of blockage. Additionally, GOQDs show a lower probability of blocking the openings of AQP1 water channels compared to GQDs, due to the hydrophobicity of the loop regions around the openings, which ultimately leads to lower interaction energy. Therefore, these findings provide new insights into the potential adverse impact of GQDs on AQP1 water channels through the blockage of their openings, offering valuable molecular insights into the toxicity profile of GQD nanomaterials.
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Affiliation(s)
- Yunbo Du
- Department of Critical Care Medicine, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China
| | - Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China.
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu Province, China
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2
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Rasoolzadeh R, Baptista L, Vajedi FS, Nikoofard V. Molecular Insights into the Binding and Conformational Changes of Hepcidin25 Blood Peptide with 4-Aminoantipyrine and Their Sorption Mechanism by Carboxylic-Functionalized Multiwalled Carbon Nanotubes: A Comprehensive Spectral Analysis and Molecular Dynamics Simulation Study. ACS OMEGA 2024; 9:35821-35836. [PMID: 39184492 PMCID: PMC11339831 DOI: 10.1021/acsomega.4c04515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024]
Abstract
In this work, the main purpose is to analyze and understand the mechanism and thermodynamic interactions of carboxylic acid-functionalized multiwalled carbon nanotubes (cf-MWCNTs) and 4-aminoantipyrine (AAP) with human hepcidine25 (Hep25) using multispectroscopic and molecular docking modeling methods, binding free energy calculations, and molecular dynamics (MD) simulations under physiological conditions. AAP belongs to a class of persistent environmental contaminants, and its residue is a potential hazard to human health, exhibiting a high binding affinity with blood peptides. Hepcidin is a 25-residue peptide hormone with four disulfide bonds that regulates the iron balance in vertebrates and contributes to host immunity as a cysteine-rich antimicrobial peptide. Due to their diverse properties and pollutant absorption capabilities, CNTs demonstrate important biological effects in biological applications, particularly in the noncovalent interactions with blood peptides. A comprehensive molecular dynamics simulation integrated with molecular docking methodologies was employed to explore the binding free energy between AAP and Hep25, identify binding sites, elucidate thermodynamic characteristics, and evaluate the binding forces governing their interaction. The investigation delved into elucidating the precise binding site of AAP within the Hep25 protein and thoroughly analyzed the impact of AAP on the microenvironment and conformational dynamics of Hep25. The circular dichroism (CD) experimental results highlight a reduction in β-sheet composition following the introduction of AAP and cf-MWCNT. In addition, outcomes from fluorescence spectroscopy demonstrate that both cf-MWCNT and AAP significantly attenuated Hep-25 fluorescence via a static quenching mechanism. According to the MD simulations, the presence of AAP induces changes in the secondary structure of Hep25 and enhances its hydrophobicity. Additionally, our findings demonstrated that alongside the alteration in protein structure and functionality induced by contaminants, cf-MWCNTs possess the capability to mitigate the contaminant-induced effects on Hep25 activity while preserving the overarching structural integrity of Hep25. Based on the distance and RDF data, we found that during the simulation the presence of the cf-MWCNT causes the AAP to move away from the Hep25, and as a result fewer and weaker interactions of the AAP with the Hep25 will be observed. Likewise, free energy calculations indicate that the binding of Hep25 to AAP and cf-MWCNT involves electrostatic, π-cationic, and π-π stacking interactions. The research findings offer invaluable insights into the intricate influence of pollutants and carbon nanotubes on protein functionality within the circulatory system and their toxicity in vivo for prospective investigations.
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Affiliation(s)
- Reza Rasoolzadeh
- Department
of Inorganic Chemistry, Institute of Chemistry, Fluminense Federal University, Niterói, Rio de Janeiro 24020-140, Brazil
| | - Leonardo Baptista
- Department
of Chemistry and Environmental, Faculty of Technology, Rio de Janeiro State University, Resende, Rio de Janeiro 27537-000, Brazil
| | - Fahimeh Sadat Vajedi
- Department
of Chemistry, Institute of Chemistry, Rio
de Janeiro State University, Rio
de Janeiro, Rio de Janeiro 20550-900, Brazil
| | - Vahid Nikoofard
- Department
of Mathematics, Physics and Computation, Faculty of Technology, Rio de Janeiro State University, Resende, Rio de Janeiro 27537-000, Brazil
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3
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Lei C, Tao M, Xu L, Yue L, Cao X, Cheng B, Wang C, Wang Z. Different functional groups of carbon dots influence the formation of protein crowns and pepsin characteristic in vitro digestion. Food Chem 2024; 440:138224. [PMID: 38134824 DOI: 10.1016/j.foodchem.2023.138224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
Application of nanomaterials (NMs) in agriculture poses an ingestion risk to humans and may affect the digestive process. Different fates of NMs with differential charges in the gastrointestinal tract should be considered. In this study, the interaction between three carbon dots (CDs) carried with different functional groups (-NH2, -OH, and -COOH) and pepsin was analyzed through an in vitro digestion model. The results showed that CDs significantly reduced pepsin activity. Among them, CDs-NH2 had the greatest effect, following by CDs-OH, and CDs-COOH. Besides, molecular docking demonstrated the specific binding site of CDs to pepsin, while the most stable binding energy (-8.10 kcal/mol) was formed between CDs-NH2 and pepsin. Further, CDs formed a nanomaterial-protein crown structure with pepsin. The present study enriches the functional group properties of CDs in the digestion and provides new ideas for the potential human health of NMs.
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Affiliation(s)
- Chunli Lei
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Mengna Tao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Lanqing Xu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Bingxu Cheng
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
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4
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Saeedimasine M, Rahmani R, Lyubartsev AP. Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. J Chem Inf Model 2024; 64:3799-3811. [PMID: 38623916 PMCID: PMC11094735 DOI: 10.1021/acs.jcim.3c01606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.
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Affiliation(s)
- Marzieh Saeedimasine
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Roja Rahmani
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
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5
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Zou F, Gu Z, Perez-Aguilar JM, Luo Y. Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure. Sci Rep 2024; 14:9168. [PMID: 38649777 PMCID: PMC11035638 DOI: 10.1038/s41598-024-59780-3] [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: 12/11/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Fluorinated graphene, a two-dimensional nanomaterial composed of three atomic layers, a central carbon layer sandwiched between two layers of fluorine atoms, has attracted considerable attention across various fields, particularly for its potential use in biomedical applications. Nonetheless, scant effort has been devoted to assessing the potential toxicological implications of this nanomaterial. In this study, we scrutinize the potential impact of fluorinated graphene on a protein model, HP35 by utilizing extensive molecular dynamics (MD) simulation methods. Our MD results elucidate that upon adsorption to the nanomaterial, HP35 undergoes a denaturation process initiated by the unraveling of the second helix of the protein and the loss of the proteins hydrophobic core. In detail, substantial alterations in various structural features of HP35 ensue, including alterations in hydrogen bonding, Q value, and RMSD. Subsequent analyses underscore that hydrophobic and van der Waals interactions (predominant), alongside electrostatic energy (subordinate), exert influence over the adsorption of HP35 on the fluorinated graphene surface. Mechanistic scrutiny attests that the unrestrained lateral mobility of HP35 on the fluorinated graphene nanomaterial primarily causes the exposure of HP35's hydrophobic core, resulting in the eventual structural denaturation of HP35. A trend in the features of 2D nanostructures is proposed that may facilitate the denaturation process. Our findings not only substantiate the potential toxicity of fluorinated graphene but also unveil the underlying molecular mechanism, which thereby holds significance for the prospective utilization of such nanomaterials in the field of biomedicine.
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Affiliation(s)
- Fangrong Zou
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), 72570, University City, Puebla, Mexico
| | - Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong Province, China.
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6
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Barria-Urenda M, Ruiz-Fernandez A, Gonzalez C, Oostenbrink C, Garate JA. Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J Chem Inf Model 2023; 63:6642-6654. [PMID: 37909535 DOI: 10.1021/acs.jcim.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.
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Affiliation(s)
- Mateo Barria-Urenda
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Doctorado en Ciencias, Mención Biofísica y Biología Computacional, Facultad de Ciencias, Universidad de Valparaíso, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Alvaro Ruiz-Fernandez
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
| | - Carlos Gonzalez
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jose Antonio Garate
- Centro Interdisciplinario de Neurociencia de Valparaíso, Pasaje Harrington 287, Playa Ancha, 2381850 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics (NNBP), Universidad San Sebastian, Bellavista, 7510602 Santiago, Chile
- Centro Científico y Tecnológico de Excelencia, Fundacion Ciencia & Vida, Santiago, Santiago 7780272, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, 7510602 Santiago, Chile
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7
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Boswell-Patterson CA, Hétu MF, Pang SC, Herr JE, Zhou J, Jain S, Bambokian A, Johri AM. Novel theranostic approaches to neovascularized atherosclerotic plaques. Atherosclerosis 2023; 374:1-10. [PMID: 37149970 DOI: 10.1016/j.atherosclerosis.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/09/2023]
Abstract
As the global burden of atherosclerotic cardiovascular disease continues to rise, there is an increased demand for improved imaging techniques for earlier detection of atherosclerotic plaques and new therapeutic targets. Plaque lesions, vulnerable to rupture and thrombosis, are thought to be responsible for the majority of cardiovascular events, and are characterized by a large lipid core, a thin fibrous cap, and neovascularization. In addition to supplying the plaque core with increased inflammatory factors, these pathological neovessels are tortuous and leaky, further increasing the risk of intraplaque hemorrhage. Clinically, plaque neovascularization has been shown to be a significant and independent predictor of adverse cardiovascular outcomes. Microvessels can be detected through contrast-enhanced ultrasound (CEUS) imaging, however, clinical assessment in vivo is generally limited to qualitative measures of plaque neovascularization. There is no validated standard for quantitative assessment of the microvessel networks found in plaques. Advances in our understanding of the pathological mechanisms underlying plaque neovascularization and its significant role in the morbidity and mortality associated with atherosclerosis have made it an attractive area of research in translational medicine. Current areas of research include the development of novel therapeutic and diagnostic agents to target plaque neovascularization stabilization. With recent progress in nanotechnology, nanoparticles have been investigated for their ability to specifically target neovascularization. Contrast microbubbles have been similarly engineered to carry loads of therapeutic agents and can be visualized using CEUS. This review summarizes the pathogenesis, diagnosis, clinical significance of neovascularization, and importantly the emerging areas of theranostic tool development.
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Affiliation(s)
| | - Marie-France Hétu
- Department of Medicine, Cardiovascular Imaging Network at Queen's (CINQ), Queen's University, Canada
| | - Stephen C Pang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Julia E Herr
- Department of Medicine, Cardiovascular Imaging Network at Queen's (CINQ), Queen's University, Canada
| | - Jianhua Zhou
- Department of Biomedical Engineering, Sun Yat-sen University, Guangzhou, China
| | - Shagun Jain
- Department of Medicine, Cardiovascular Imaging Network at Queen's (CINQ), Queen's University, Canada
| | - Alexander Bambokian
- Department of Medicine, Cardiovascular Imaging Network at Queen's (CINQ), Queen's University, Canada
| | - Amer M Johri
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada; Department of Medicine, Cardiovascular Imaging Network at Queen's (CINQ), Queen's University, Canada.
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8
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Dai X, Chen Y. Computational Biomaterials: Computational Simulations for Biomedicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2204798. [PMID: 35916024 DOI: 10.1002/adma.202204798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/23/2022] [Indexed: 05/14/2023]
Abstract
With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.
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Affiliation(s)
- Xinyue Dai
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai, 200444, P. R. China
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9
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Computational Investigation of Chirality-Based Separation of Carbon Nanotubes Using Tripeptide Library. Biomolecules 2023; 13:biom13010175. [PMID: 36671560 PMCID: PMC9855824 DOI: 10.3390/biom13010175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Carbon nanotubes (CNT) have fascinating applications in flexible electronics, biosensors, and energy storage devices, and are classified as metallic or semiconducting based on their chirality. Semiconducting CNTs have been teased as a new material for building blocks in electronic devices, owing to their band gap resembling silicon. However, CNTs must be sorted into metallic and semiconducting for such applications. Formerly, gel chromatography, ultracentrifugation, size exclusion chromatography, and phage display libraries were utilized for sorting CNTs. Nevertheless, these techniques are either expensive or have poor efficiency. In this study, we utilize a novel technique of using a library of nine tripeptides with glycine as a central residue to study the effect of flanking residues for large-scale separation of CNTs. Through molecular dynamics, we found that the tripeptide combinations with threonine as one of the flanking residues have a high affinity for metallic CNTs, whereas those with flanking residues having uncharged and negatively charged polar groups show selectivity towards semiconducting CNTs. Furthermore, the role of interfacial water molecules and the ability of the tripeptides to form hydrogen bonds play a crucial role in sorting the CNTs. It is envisaged that CNTs can be sorted based on their chirality-selective interaction affinity to tripeptides.
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10
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Huang W, Wang Z, Luo J. Molecular Dynamics Study of the Curvature-Driven Interactions between Carbon-Based Nanoparticles and Amino Acids. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020482. [PMID: 36677540 PMCID: PMC9861389 DOI: 10.3390/molecules28020482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
We researched the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional graphene (graphene33). Their curvatures decrease sequentially, and all of the CNTs are single-walled carbon nanotubes. We observed that as the curvature of CBNs decreases, the adsorption effect of the 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and "Benzene-like" Pro also have a strong adsorption effect on carbon-based nanoparticles.
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Affiliation(s)
- Wanying Huang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China
- Zhejiang Lab, Nanhu-Kechuang Avenue, Yuhang District, Hangzhou 310000, China
| | - Zhenyu Wang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China
| | - Junyan Luo
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310000, China
- Correspondence:
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11
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Tiwari S, Chopra L. Therapeutic nanoparticles for targeted drug delivery: A mini-review. AIP CONFERENCE PROCEEDINGS 2023; 2773:060005. [DOI: 10.1063/5.0113615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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12
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Villari V. Molecular and Macromolecular Interactions of Carbon-Based Nanostructures. Int J Mol Sci 2022; 24:ijms24010619. [PMID: 36614062 PMCID: PMC9820210 DOI: 10.3390/ijms24010619] [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: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
The interactions of molecules and macromolecules with carbon nanostructures such as carbon dots, carbon nanotubes, graphene, graphene oxide, and fullerenes, have been stimulating the interest of the researchers working on the preparation, functionalization, properties and applications of carbon-based nanomaterials [...].
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Affiliation(s)
- Valentina Villari
- CNR-Istituto per i Processi Chimico-Fisici, Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy
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13
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Packirisamy V, Pandurangan P. Interaction of Atomically Precise Thiolated Copper Nanoclusters with Proteins: A Comparative Study. ACS OMEGA 2022; 7:42550-42559. [PMID: 36440105 PMCID: PMC9685744 DOI: 10.1021/acsomega.2c06011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
A facile synthesis of glutathione-stabilized copper nanoclusters (CuNCs) is carried out in H2O/ tetrahydrofuran medium. The photophysical and morphological studies performed with as-synthesized CuNCs revealed the formation of green-emissive, stable, and smaller nanoclusters. The precise composition of these as-synthesized CuNCs was predicted with the aid of electrospray ionization mass spectrometry analysis as Cu12(SG)9. Furthermore, the systematic studies of the interaction of synthesized CuNCs with three plasmatic proteins, namely, bovine serum albumin (BSA), lysozyme (Lys), and hemoglobin (Hb) have been performed by using a series of spectroscopic studies. The conformational changes in these proteins upon interacting with CuNCs and their binding stoichiometries have been investigated from the combination of UV-visible and steady-state fluorescence measurements. The changes in the microenvironment of proteins caused by CuNCs were investigated by circular dichroism spectroscopy. Among these three proteins, BSA and Lys had a minor effect on the luminescence of CuNCs, which makes them suitable candidates for biological applications. There are no drastic changes in the microenvironment of NCs as well as proteins because of the possibilities of weak electrostatic and H-bonding interactions of CuNCs with BSA and Lys. The feasibility of strong metallophic interaction between the Fe2+ present in the heme group of Hb and Cu(I) or -S atoms present in the CuNCs brings considerable changes in the photophysical activity of CuNCs and their interactions with Hb. The functional groups on NCs as well as active amino acid residues present in proteins play a crucial role in determining their interactions. This work shed a piece of knowledge on designing NCs for specific biological applications.
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Affiliation(s)
- Vinitha Packirisamy
- Department of Physical Chemistry,
School of Chemical Science, University of
Madras, Guindy Campus, Chennai, Tamilnadu600 025, India
| | - Prabhu Pandurangan
- Department of Physical Chemistry,
School of Chemical Science, University of
Madras, Guindy Campus, Chennai, Tamilnadu600 025, India
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14
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Yang X, Zhang X, Shu X, Zhang W, Kai J, Tang M, Gong J, Yang J, Lin J, Chai Y, Liu J. Effects of multi-walled carbon nanotubes in soil on earthworm growth and reproduction, enzymatic activities, and metabolomics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114158. [PMID: 36228358 DOI: 10.1016/j.ecoenv.2022.114158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Increased production and environmental release of multi-walled carbon nanotubes (MWCNTs) increase soil exposure and potential risk to earthworms. However, MWCNT toxicity to earthworms remains unclear, with some studies identifying negative effects and others negligible effects. In this study, to determine whether exposure to MWCNTs negatively affects earthworms and to elucidate possible mechanisms of toxicity, earthworms were exposed to sublethal soil concentrations of MWCNTs (10, 50, and 100 mg/kg) for 28 days. Earthworm growth and reproduction, activities of cytochrome P450 (CYP) isoforms (1A2, 2C9, and 3A4) and antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and glutathione-s-transferase (GST)), and metabolomics were determined. Effects of MWCNTs on earthworms depended on exposure concentration. Exposure to MWCNTs did not significantly affect growth and reproduction of individual earthworms. Exposure to 50 mg/kg MWCNTs significantly increased activities of CYP2C9, CYP3A4, SOD, CAT, and GST but clearly reduced levels of L-aspartate, L-asparagine, and glutamine. With exposure to 100 mg/kg MWCNTs, toxic effects on earthworms were observed, with significant inhibition in activities of CYP isoenzymes and SOD, significant reductions in L-aspartate, L-asparagine, glutamine, and tryptophan, and simultaneous accumulations of citrate, isocitrate, fumarate, 2-oxoglutarate, pyruvate, D-galactose, carbamoyl phosphate, formyl anthranilate, hypoxanthine, and xanthine. Results suggest that toxicity of MWCNTs to earthworms is associated with reduced detoxification capacity, excessive oxidative stress, and disturbance of multiple metabolic pathways, including amino acids metabolism, the tricarboxylic acid cycle, pyruvate metabolism, D-galactose metabolism, and purine metabolism. The study provides new insights to better understand and predict the toxicity of MWCNTs in soil.
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Affiliation(s)
- Xiaoxia Yang
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China.
| | - Xuemei Zhang
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Xiao Shu
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Wei Zhang
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Jianrong Kai
- Institute of Quality Standard and Testing Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Mingfeng Tang
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China.
| | - Jiuping Gong
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Junying Yang
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Junjie Lin
- Institute of Quality Standard and Testing Technology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Yong Chai
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
| | - Jianfei Liu
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, Chongqing 401329, People's Republic of China; Key Laboratory of Water, Environment, Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Chongqing 404100, People's Republic of China
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15
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Rajan D, Rajamanikandan R, Ilanchelian M. Morphological and biophysical insights into the gold nanorods binding interaction of haemoglobin/myoglobin by hybrid spectroscopic approaches with bacterial cytotoxicity evaluation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Huang W, Ou X, Luo J. Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids. Molecules 2022; 27:2785. [PMID: 35566140 PMCID: PMC9104776 DOI: 10.3390/molecules27092785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation; that is, the target distribution function and the PMF potential energy are extracted, and then, the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have been through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.
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Affiliation(s)
- Wanying Huang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China;
| | - Xinwen Ou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China;
| | - Junyan Luo
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310023, China
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17
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Siani P, Di Valentin C. Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO 2 nanoparticles. NANOSCALE 2022; 14:5121-5137. [PMID: 35302136 PMCID: PMC8969454 DOI: 10.1039/d1nr07647g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO2 nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.
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Affiliation(s)
- Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy.
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, 20125 Milano, Italy.
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18
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Zhang C, Zhou X, Zhang H, Han X, Li B, Yang R, Zhou X. Recent Progress of Novel Nanotechnology Challenging the Multidrug Resistance of Cancer. Front Pharmacol 2022; 13:776895. [PMID: 35237155 PMCID: PMC8883114 DOI: 10.3389/fphar.2022.776895] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance (MDR) of tumors is one of the clinical direct reasons for chemotherapy failure. MDR directly leads to tumor recurrence and metastasis, with extremely grievous mortality. Engineering a novel nano-delivery system for the treatment of MDR tumors has become an important part of nanotechnology. Herein, this review will take those different mechanisms of MDR as the classification standards and systematically summarize the advances in nanotechnology targeting different mechanisms of MDR in recent years. However, it still needs to be seriously considered that there are still some thorny problems in the application of the nano-delivery system against MDR tumors, including the excessive utilization of carrier materials, low drug-loading capacity, relatively narrow targeting mechanism, and so on. It is hoped that through the continuous development of nanotechnology, nano-delivery systems with more universal uses and a simpler preparation process can be obtained, for achieving the goal of defeating cancer MDR and accelerating clinical transformation.
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Affiliation(s)
- Chengyuan Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Xuemei Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Hanyi Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Xuanliang Han
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Baijun Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Ran Yang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
| | - Xing Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing, China
- Department of Pharmacy, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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19
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Veltman B, Harpaz D, Cohen Y, Poverenov E, Eltzov E. Characterization of the selective binding of modified chitosan nanoparticles to Gram-negative bacteria strains. Int J Biol Macromol 2022; 194:666-675. [PMID: 34822835 DOI: 10.1016/j.ijbiomac.2021.11.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/12/2021] [Accepted: 11/16/2021] [Indexed: 01/24/2023]
Abstract
Chitosan is a nature-sourced polysaccharide widely used in numerous applications. The antibacterial potential of chitosan has attracted researchers to further develop and utilize this polymer for the formation of biocompatible antibacterial agents for both the food and healthcare industries. The tested hypothesis in this study is that modified N-alkylaminated chitosan nanoparticles (CNPs) have selective binding properties to Gram-negative bacteria strains that result in bacterial aggregation. Various bacterial strains were tested of five Gram-negative bacteria including Erwinia carotovora, Escherichia coli, Pseudomonas aeruginosa, Salmonella, and Serratia marcescens, as well as three Gram-positive bacteria strains including Bacillus licheniformis, Bacillus megaterium, and Bacillus subtilis. The fluorescence microscopy characterization showed that the presence of CNPs caused the aggregation of Escherichia coli bacteria cells, where modified CNPs with a shorter chain length of the substituent caused a higher aggregation effect. Moreover, it was found that the CNPs exhibited a selective binding behavior to Gram-negative as compared to Gram-positive bacteria strains, mainly to Escherichia coli and Salmonella. Also, the scanning electron microscopy characterization showed that CNPs exhibited selective binding to Gram-negative bacteria, which was especially understood when both Gram-negative and Gram-positive bacteria strains were within the same sample. In addition, the bacterial viability assay suggests that CNPs with a lower degree of substitution have a higher inhibitory effect on bacterial growth. CNPs with longer side chains had a less inhibitory effect on the bacterial growth of Gram-negative strains, where a concentration-dependent response pattern was only seen for the cases of Gram-negative strains, and not for the case of Gram-positive strain. To conclude, the further understanding of the selective binding of CNPs to Gram-negative bacteria strains may produce new opportunities for the discovery and characterization of effective antibacterial agents.
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Affiliation(s)
- Boris Veltman
- Institute of Postharvest and Food Science, Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Dorin Harpaz
- Institute of Postharvest and Food Science, Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Yael Cohen
- Institute of Postharvest and Food Science, Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel.
| | - Elena Poverenov
- Institute of Postharvest and Food Science, Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel; Agro-Nanotechnology and Advanced Materials Research Center, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel.
| | - Evgeni Eltzov
- Institute of Postharvest and Food Science, Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel; Agro-Nanotechnology and Advanced Materials Research Center, Volcani Institute, Agricultural Research Organization, Rishon LeZion 7505101, Israel.
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20
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Fang B, Dai X, Li B, Qu Y, Li YQ, Zhao M, Yang Y, Li W. Self-assembly of ultra-small-sized carbon nanoparticles in lipid membrane disrupts its integrity. NANOSCALE ADVANCES 2021; 4:163-172. [PMID: 36132950 PMCID: PMC9417506 DOI: 10.1039/d1na00529d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/12/2021] [Indexed: 06/15/2023]
Abstract
Although nanomaterials are widely studied in biomedical applications, the major concern of nanotoxicity still exists. Therefore, numerous studies have been conducted on the interactions of various biomolecules with various types of nanomaterials, including carbon nanotubes, graphene, fullerene etc. However, the size effect of nanomaterials is poorly documented, especially ultra-small particles. Here, the interactions of the smallest carbon nanoparticle (NP), C28, with the cell membrane were studied using molecular dynamics (MD) simulations. The results show that similar to fullerene C60, the C28 NPs can self-assemble into stable clusters in water. Inside the membrane, the C28 NPs are more prone to aggregate to form clusters than C60 NPs. The reason for C28 aggregation is characterized by the potential of mean force (PMF) and can be explained by the polarized nature of C28 NPs while the acyl chains of lipids are nonpolar. At the C28 cluster regions, the thickness of the membrane is significantly reduced by the C28 aggregation. Accordingly, the membrane loses its structural integrity, and translocation of water molecules through it was observed. Thus, these results predict a stronger cytotoxicity to cells than C60 NPs. The present findings might shed light on the understanding of the cytotoxicity of NPs with different sizes and would be helpful for the potential biomedical applications of carbon NPs, especially as antibacterial agents.
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Affiliation(s)
- Bing Fang
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Xing Dai
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University Suzhou 215123 China
| | - Baoyu Li
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University Suzhou 215123 China
| | - Yuanyuan Qu
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Yong-Qiang Li
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Mingwen Zhao
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Normal University Jinan 250014 China
| | - Weifeng Li
- School of Physics, Shandong University Jinan Shandong 250100 China
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21
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Bao L, Cui X, Wang X, Wu J, Guo M, Yan N, Chen C. Carbon Nanotubes Promote the Development of Intestinal Organoids through Regulating Extracellular Matrix Viscoelasticity and Intracellular Energy Metabolism. ACS NANO 2021; 15:15858-15873. [PMID: 34622660 DOI: 10.1021/acsnano.1c03707] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The biological effect of engineered carbon nanotubes (CNTs) as beneficial biomaterials on the intestine, especially on its development, remains unclear. Here, we investigated the profitable effect of CNTs with a different graphene layer and surface modification on the 3D model of intestinal organoids and demonstrated that CNTs (50 μg/mL) promoted the development of intestinal organoids over time (0-5 days). The mechanisms involve the modulation of extracellular matrix (ECM) viscoelasticity and intracellular energy metabolism. In particular, CNTs reduced the hardness of the extracellular matrix through decreasing the elasticity and increasing the viscosity as a result of elevated metalloproteinase and binding to a protein scaffold, which activated the mechanical membrane sensors of cells, Piezo, and downstream P-p38-yes-associated protein (YAP) pathway. Moreover, CNTs altered the metabolic profile of intestinal organoids and induced increased mitochondria activity, respiration, and nutrient absorption. These mechanisms cooperated with each other to promote the proliferation and differentiation of intestinal organoids. In addition, the promoted effect of CNTs is highly dependent on the number of graphene layers, manifested as multiwalled CNTs > single-walled CNTs. Our findings highlight the CNT-intestine interaction and imply the potential of CNTs as biomaterials for intestine-associated tissue engineering.
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Affiliation(s)
- Lin Bao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuejing Cui
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong 510700, China
| | - Xiaoyu Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junguang Wu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengyu Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Na Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences (CAS), Beijing 100190, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong 510700, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Marforio TD, Calza A, Mattioli EJ, Zerbetto F, Calvaresi M. Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C 60. Int J Mol Sci 2021; 22:ijms222111567. [PMID: 34768997 PMCID: PMC8583719 DOI: 10.3390/ijms222111567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/05/2023] Open
Abstract
Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C60 was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C60 binding.
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23
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Wang X, Zhang G, Yu D, Wang N, Guan Q. The interaction of folate-modified Bletilla striata polysaccharide-based micelle with bovine serum albumin. Glycoconj J 2021; 38:585-597. [PMID: 34586534 DOI: 10.1007/s10719-021-10022-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/19/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022]
Abstract
We fabricated an amphiphilic folate-modified Bletilla striata polysaccharide (FA-BSP-SA) copolymer that exhibited good biocompatibility and superior antitumor effects. This study investigated the affinity between FA-BSP-SA and bovine serum albumin (BSA) via multispetroscopic approaches. Changes in the morphology and particle size showed that FA-BSP-SA formed a blurry "protein corona". Stern-Volmer equation demonstrated that FA-BSP-SA micelles decreased the fluorescence of BSA via static quenching. The measurement results of thermodynamic parameters (entropy change, enthalpy change, and Gibbs free energy) suggested that the binding between FA-BSP-SA and BSA was spontaneous in which Van der Waals forces and hydrogen bonding played major roles. The results from synchronous fluorescence, circular dichroism, and UV spectra also revealed that BSA conformation was slightly altered by decreasing α-helical contents. In addition, the antitumor effects in vitro of Dox@FA-BSP-SA micelles and the cellular uptake behavior of micelles in 4T1 cells were decreased after incubating with BSA.
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Affiliation(s)
- Xinying Wang
- Department of Pharmaceutics, School of Pharmacy, Jilin University, No. 1266, Fujin Road, Changchun, 130021, China
| | - Guangyuan Zhang
- Department of Pharmaceutics, School of Pharmacy, Jilin University, No. 1266, Fujin Road, Changchun, 130021, China
| | - Di Yu
- Department of Pharmaceutics, School of Pharmacy, Jilin University, No. 1266, Fujin Road, Changchun, 130021, China
| | - Ning Wang
- Department of Pharmaceutics, School of Pharmacy, Jilin University, No. 1266, Fujin Road, Changchun, 130021, China
| | - Qingxiang Guan
- Department of Pharmaceutics, School of Pharmacy, Jilin University, No. 1266, Fujin Road, Changchun, 130021, China.
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24
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Huang S, Deng Y, Xu J, Liu J, Liu L, Fan C. The Role of Exosomes and Their Cargos in the Mechanism, Diagnosis, and Treatment of Atrial Fibrillation. Front Cardiovasc Med 2021; 8:712828. [PMID: 34395566 PMCID: PMC8355361 DOI: 10.3389/fcvm.2021.712828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Atrial fibrillation (AF) is the most common persistent arrhythmia, but the mechanism of AF has not been fully elucidated, and existing approaches to diagnosis and treatment face limitations. Recently, exosomes have attracted considerable interest in AF research due to their high stability, specificity and cell-targeting ability. The aim of this review is to summarize recent literature, analyze the advantages and limitations of exosomes, and to provide new ideas for their use in understanding the mechanism and improving the diagnosis and treatment of AF.
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Affiliation(s)
- Shengyuan Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yating Deng
- Xiangya Medical College of Central South University, Changsha, China
| | - Jiaqi Xu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Jiachen Liu
- Xiangya Medical College of Central South University, Changsha, China
| | - Liming Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chengming Fan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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Nabi SU, Ali SI, Rather MA, Sheikh WM, Altaf M, Singh H, Mumtaz PT, Mishra NC, Nazir SU, Bashir SM. Organoids: A new approach in toxicity testing of nanotherapeutics. J Appl Toxicol 2021; 42:52-72. [PMID: 34060108 DOI: 10.1002/jat.4206] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022]
Abstract
Nanotechnology has revolutionized diverse fields, which include agriculture, the consumer market, medicine, and other fields. Widespread use of nanotechnology-based products has led to increased prevalence of these novel formulations in the environment, which has raised concerns regarding their deleterious effects. The application of nanotechnology-based formulations into clinical use is hampered by the lack of the availability of effective in vitro systems, which could accurately assess their in vivo toxic effects. A plethora of studies has shown the hazardous effects of nanoparticle-based formulations in two-dimensional in vitro cell cultures and animal models. These have some associated disadvantages when used for the evaluation of nano-toxicity. Organoid technology fills the space between existing two-dimensional cell line culture and in vivo models. The uniqueness of organoids over other systems for evaluating toxicity caused by nano-drug formulation includes them being a co-culture of diverse cell types, dynamic flow within them that simulates the actual flow of nanoparticles within biological systems, extensive cell-cell, cell-matrix interactions, and a tissue-like morphology. Thus, it mimics the actual tissue microenvironment and, subsequently, provides an opportunity to study drug metabolism and toxico-dynamics of nanotechnology-based novel formulations. The use of organoids in the evaluation of nano-drug toxicity is in its infancy. A limited number of studies conducted so far have shown good predictive value and efficiently significant data correlation with the clinical trials. In this review, we attempt to introduce organoids of the liver, lungs, brain, kidney intestine, and potential applications to evaluate toxicity caused by nanoparticles.
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Affiliation(s)
- Showkat Ul Nabi
- Large Animal Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Ethics & Jurisprudence, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Sofi Imtiyaz Ali
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Muzafar Ahmad Rather
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Wajid Mohammad Sheikh
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Mehvish Altaf
- Department of Food Technology, Islamic University of Science & Technology, Awantipora, Pulwama, Jammu and Kashmir, India
| | - Hemant Singh
- Department of Polymer and Process Engineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Peerzada Tajamul Mumtaz
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Narayan Chandra Mishra
- Department of Polymer and Process Engineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sheikh Uzma Nazir
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Showkeen Muzamil Bashir
- Biochemistry & Molecular Biology Lab, Division of Veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
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Akhuli A, Chakraborty D, Agrawal AK, Sarkar M. Probing the Interaction of Bovine Serum Albumin with Copper Nanoclusters: Realization of Binding Pathway Different from Protein Corona. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1823-1837. [PMID: 33502208 DOI: 10.1021/acs.langmuir.0c03176] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With an aim to understand the interaction mechanism of bovine serum albumin (BSA) with copper nanoclusters (CuNCs), three different types CuNCs having chemically different surface ligands, namely, tannic acid (TA), chitosan, and cysteine (Cys), have been fabricated, and investigations are carried out in the absence and presence of protein (BSA) at ensemble-averaged and single-molecule levels. The CuNCs, capped with different surface ligands, are consciously chosen so that the role of surface ligands in the overall protein-NCs interactions is clearly understood, but, more importantly, to find whether these CuNCs can interact with protein in a new pathway without forming the "protein corona", which otherwise has been observed in relatively larger nanoparticles when they are exposed to biological fluids. Analysis of the data obtained from fluorescence, ζ-potential, and ITC measurements has clearly indicated that the BSA protein in the presence of CuNCs does not attain the binding stoichiometry (BSA/CuNCs > 1) that is required for the formation of "protein corona". This conclusion is further substantiated by the outcome of the fluorescence correlation spectroscopy (FCS) study. Further analysis of data and thermodynamic calculations have revealed that the surface ligands of the CuNCs play an important role in the protein-NCs binding events, and they can alter the mode and thermodynamics of the process. Specifically, the data have demonstrated that the binding of BSA with TA-CuNCs and Chitosan-CuNCs follows two types of binding modes; however, the same with Cys-CuNCs goes through only one type of binding mode. Circular dichroism (CD) measurements have indicated that the basic structure of BSA remains almost unaltered in the presence of CuNCs. The outcome of the present study is expected to encourage and enable better application of NCs in biological applications.
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Affiliation(s)
- Amit Akhuli
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Debabrata Chakraborty
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Aman Kumar Agrawal
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
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Roacho-Pérez JA, Rodríguez-Aguillón KO, Gallardo-Blanco HL, Velazco-Campos MR, Sosa-Cruz KV, García-Casillas PE, Rojas-Patlán L, Sánchez-Domínguez M, Rivas-Estilla AM, Gómez-Flores V, Chapa-Gonzalez C, Sánchez-Domínguez CN. A Full Set of In Vitro Assays in Chitosan/Tween 80 Microspheres Loaded with Magnetite Nanoparticles. Polymers (Basel) 2021; 13:polym13030400. [PMID: 33513783 PMCID: PMC7865444 DOI: 10.3390/polym13030400] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Microspheres have been proposed for different medical applications, such as the delivery of therapeutic proteins. The first step, before evaluating the functionality of a protein delivery system, is to evaluate their biological safety. In this work, we developed chitosan/Tween 80 microspheres loaded with magnetite nanoparticles and evaluated cell damage. The formation and physical-chemical properties of the microspheres were determined by FT-IR, Raman, thermogravimetric analysis (TGA), energy-dispersive X-ray spectroscopy (EDS), dynamic light scattering (DLS), and SEM. Cell damage was evaluated by a full set of in vitro assays using a non-cancerous cell line, human erythrocytes, and human lymphocytes. At the same time, to know if these microspheres can load proteins over their surface, bovine serum albumin (BSA) immobilization was measured. Results showed 7 nm magnetite nanoparticles loaded into chitosan/Tween 80 microspheres with average sizes of 1.431 µm. At concentrations from 1 to 100 µg/mL, there was no evidence of changes in mitochondrial metabolism, cell morphology, membrane rupture, cell cycle, nor sister chromatid exchange formation. For each microgram of microspheres 1.8 µg of BSA was immobilized. The result provides the fundamental understanding of the in vitro biological behavior, and safety, of developed microspheres. Additionally, this set of assays can be helpful for researchers to evaluate different nano and microparticles.
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Affiliation(s)
- Jorge A Roacho-Pérez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (J.A.R.-P.); (K.O.R.-A.); (A.M.R.-E.)
| | - Kassandra O Rodríguez-Aguillón
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (J.A.R.-P.); (K.O.R.-A.); (A.M.R.-E.)
| | - Hugo L Gallardo-Blanco
- Departamento de Genética, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (H.L.G.-B.); (M.R.V.-C.); (L.R.-P.)
| | - María R Velazco-Campos
- Departamento de Genética, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (H.L.G.-B.); (M.R.V.-C.); (L.R.-P.)
| | - Karla V Sosa-Cruz
- Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez 32310, Mexico; (K.V.S.-C.); (P.E.G.-C.); (V.G.-F.)
| | - Perla E García-Casillas
- Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez 32310, Mexico; (K.V.S.-C.); (P.E.G.-C.); (V.G.-F.)
| | - Luz Rojas-Patlán
- Departamento de Genética, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (H.L.G.-B.); (M.R.V.-C.); (L.R.-P.)
| | - Margarita Sánchez-Domínguez
- Centro de Investigación en Materiales Avanzados, S.C. (CIMAV, S.C.), Unidad Monterrey, Apodaca 66628, Mexico;
| | - Ana M Rivas-Estilla
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (J.A.R.-P.); (K.O.R.-A.); (A.M.R.-E.)
| | - Víctor Gómez-Flores
- Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez 32310, Mexico; (K.V.S.-C.); (P.E.G.-C.); (V.G.-F.)
| | - Christian Chapa-Gonzalez
- Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez 32310, Mexico; (K.V.S.-C.); (P.E.G.-C.); (V.G.-F.)
- Correspondence: (C.C.-G.); (C.N.S.-D.)
| | - Celia N Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (J.A.R.-P.); (K.O.R.-A.); (A.M.R.-E.)
- Correspondence: (C.C.-G.); (C.N.S.-D.)
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Wang Z, Zhou X, Zuo G. EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space. Front Mol Biosci 2020; 7:589718. [PMID: 33195438 PMCID: PMC7653181 DOI: 10.3389/fmolb.2020.589718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/24/2020] [Indexed: 11/27/2022] Open
Abstract
The transition network provides a key to reveal the thermodynamic and kinetic properties of biomolecular systems. In this paper, we introduce a new method, named effective energy rescaling space trajectory mapping (EspcTM), to detect metastable states and construct transition networks based on the simulation trajectories of the complex biomolecular system. It mapped simulation trajectories into an orthogonal function space, whose bases were rescaled by effective energy, and clustered the interrelation between these trajectories to locate metastable states. By using the EspcTM method, we identified the metastable states and elucidated interstate transition kinetics of a Brownian particle and a dodecapeptide. It was found that the scaling parameters of effective energy also provided a clue to the dominating factors in dynamics. We believe that the EspcTM method is a useful tool for the studies of dynamics of the complex system and may provide new insight into the understanding of thermodynamics and kinetics of biomolecular systems.
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Affiliation(s)
- Zhenyu Wang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guanghong Zuo
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
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29
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Jia X, Yang Y, Liu Y, Niu W, Li YQ, Zhao M, Mu Y, Li W. Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping. NANOSCALE ADVANCES 2020; 2:4539-4546. [PMID: 36132907 PMCID: PMC9417744 DOI: 10.1039/d0na00365d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/25/2020] [Indexed: 06/16/2023]
Abstract
In recent years, nanomaterials have attracted considerable research attention for biological and medical related applications due to their well-recognized physical and chemical properties. However, the deep understanding of the binding process at the protein-nanomaterial interface is essential to solve the concern of nano-toxicity. Here, we study the interactions between the recently reported graphenic nano-sheets, BC3 and C3N, and a prototypical protein (YAP65WW domain) via atomistic molecular dynamics simulations. Our simulations reveal that elemental doping is an effective way to tune the binding characteristics of YAP65WW with two nanomaterials. While YAP65WW can be attracted by two nanomaterials, the BC3 sheet is less able to disrupt the protein structure than C3N. From the energy point of view, this is because protein residues demonstrate a binding preference with the trend from electron rich nitrogen to electron deficient boron. Structural analyses of the bio-nano interface revealed the formation of an ordered water shell on the BC3 surface, which was compatible to the crystal pattern of BC3. When a protein binds with BC3, these interfacial water molecules protect the protein from being disrupted. We suggest that elemental doping is efficient to produce fruitful biological-effects of graphenic nanomaterials, which make it a prospective solution for the future design and fabrication of advanced nanomaterials with desired function.
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Affiliation(s)
- Xiao Jia
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yang Liu
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Weihua Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yong-Qiang Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Mingwen Zhao
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University 637551 Singapore
| | - Weifeng Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
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30
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Zhu S, Li L, Gu Z, Chen C, Zhao Y. 15 Years of Small: Research Trends in Nanosafety. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000980. [PMID: 32338444 DOI: 10.1002/smll.202000980] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
In the field of nano- and microscale science and technology, Small has become one of the worldwide leading journals since its initiation 15 years ago. Among all the topics covered in Small, "nanosafety" has received growing interest over the years, which accounts for a large proportion of the total publications of Small. Herein, inspired by its coming Special Issue "Rethinking Nanosafety," a general bibliometric overview of the nanosafety studies that have been published in Small is presented. Using the data derived from the Web of Science Core Collection, the annual publication growth, most influential countries/institutions as well as the visualized collaborations between different countries and institutions based on CiteSpace software are presented. A special emphasis on the impact of the previous Special Issue from Small that is related to nanosafety research is given and the research trend from the most highly cited papers during last 15 years is analyzed. Lastly, future research directions are also proposed.
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Affiliation(s)
- Shuang Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics and National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Science, Beijing, 100190, China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics and National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Science, Beijing, 100190, China
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Science, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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32
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Zhou R, Weikl T, Ma YQ. Theoretical modeling of interactions at the bio-nano interface. NANOSCALE 2020; 12:10426-10429. [PMID: 32393940 DOI: 10.1039/d0nr90092c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ruhong Zhou, Thomas Weikl and Yu-qiang Ma introduce the Nanoscale themed issue on Theoretical Modelling at Biointerfaces.
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Affiliation(s)
- Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China. and Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Thomas Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, Potsdam, Germany.
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
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Tong J, Zhang P, Zhang L, Zhang D, Beratan DN, Song H, Wang Y, Li T. A Robust Bioderived Wavelength-Specific Photosensor Based on BLUF Proteins. SENSORS AND ACTUATORS. B, CHEMICAL 2020; 310:127838. [PMID: 32296265 PMCID: PMC7157799 DOI: 10.1016/j.snb.2020.127838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photosensitive proteins are naturally evolved photosensors that often respond to light signals of specific wavelengths. However, their poor stability under ambient conditions hinders their applications in non-biological settings. In this proof-of-principle study, we grafted the blue light using flavin (BLUF) protein reconstructed with flavin adenine dinucleotide (FAD) or roseoflavin (RoF) onto pristine graphene, and achieved selective sensitivity at 450 nm or 500 nm, respectively. We improved the thermal and operational stability substantially via structure-guided cross-linking, achieving 6-month stability under ambient condition and normal operation at temperatures up to 200 °C. Furthermore, the device exhibited rare negative photoconductivity behavior. The origins of this negative photoconductivity behavior were elucidated via a combination of experimental and theoretical analysis. In the photoelectric conversion studies, holes from photoexcited flavin migrated to graphene and recombined with electrons. The device allows facile modulation and detection of charge transfer, and provides a versatile platform for future studies of photoinduced charge transfer in biosensors as well as the development of stable wavelength-selective biophotosensors.
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Affiliation(s)
- Jing Tong
- Science and Technology on Microsytem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Lei Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Dongwei Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Haifeng Song
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- National engineering research center for protein drugs (NERCPD), Beijing 102206, China
| | - Tie Li
- Science and Technology on Microsytem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
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34
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Ahmadi S, Yousef Mardoukhi MS, Salehi M, Sajjadi S, Keihan AH. Molecular dynamics simulation of lactate dehydrogenase adsorption onto pristine and carboxylic-functionalized graphene. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1632447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Salman Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Mahmoud Salehi
- Department of Biology, Faculty of Science and Engineering, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Sharareh Sajjadi
- Department of Biology, Roudehen Branch, Islamic Azad University, Roudehen, Iran
| | - Amir Homayoun Keihan
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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35
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Song J, Wang Q, Zeng Y, Liu Y, Jiang W. Deposition of protein-coated multi-walled carbon nanotubes on oxide surfaces and the retention in a silicon micromodel. JOURNAL OF HAZARDOUS MATERIALS 2019; 375:107-114. [PMID: 31054527 DOI: 10.1016/j.jhazmat.2019.04.077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 05/09/2023]
Abstract
The aggregation, deposition and porous retention of bovine serum albumin treated multi-walled carbon nanotubes (BSA-MWCNTs) are investigated using dynamic light scattering (DLS), quartz crystal microbalance with dissipation (QCM-D) and 2-dimensional silicon micromodel, respectively. The aggregation of BSA-MWCNTs is consistent with Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The critical coagulation concentration (CCC) is 175 mM NaCl and 2.7 mM CaCl2, suggesting that Ca2+ causes stronger aggregation. The BSA-MWCNT deposition on SiO2 surface is unfavorable with critical deposition concentration (CDC) of 100 mM in NaCl and 0.9 mM in CaCl2. The deposition on the Al2O3 surface is favorable. Deposition rate is dominated by electrostatic forces at low ionic strength (IS), but electrostatic interaction is eliminated when IS is above CDC. Therefore the deposition rate on SiO2 or Al2O3 surface starts decreasing at the CDC point due to the reduced particle diffusion. In micromodel, the amount and position of attached BSA-MWCNTs in pore space can be observed by a microscope. The retention attachment efficiency increases at higher IS. The suspended BSA-MWCNTs approach to the collector through either diffusion or interception. The attached BSA-MWCNTs narrow the pore space and then clog the pore throats. The straining process happens on the clogged pore throats.
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Affiliation(s)
- Jian Song
- Environment Research Institute, Shandong University, Qingdao 266237, China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, China
| | - Qi Wang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Yuxuan Zeng
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Yuanyuan Liu
- School of Earth Science and Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Jiang
- Environment Research Institute, Shandong University, Qingdao 266237, China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, China.
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Keshavan S, Calligari P, Stella L, Fusco L, Delogu LG, Fadeel B. Nano-bio interactions: a neutrophil-centric view. Cell Death Dis 2019; 10:569. [PMID: 31358731 PMCID: PMC6662811 DOI: 10.1038/s41419-019-1806-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/04/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022]
Abstract
Neutrophils are key components of the innate arm of the immune system and represent the frontline of host defense against intruding pathogens. However, neutrophils can also cause damage to the host. Nanomaterials are being developed for a multitude of different purposes and these minute materials may find their way into the body through deliberate or inadvertent exposure; understanding nanomaterial interactions with the immune system is therefore of critical importance. However, whereas numerous studies have focused on macrophages, less attention is devoted to nanomaterial interactions with neutrophils, the most abundant leukocytes in the blood. We discuss the impact of engineered nanomaterials on neutrophils and how neutrophils, in turn, may digest certain carbon-based materials such as carbon nanotubes and graphene oxide. We also discuss the role of the corona of proteins adsorbed onto the surface of nanomaterials and whether nanomaterials are sensed as pathogens by cells of the immune system.
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Affiliation(s)
- Sandeep Keshavan
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Calligari
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Laura Fusco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Lucia Gemma Delogu
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | - Bengt Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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37
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Liu Y, Li S, Liu X, Sun H, Yue T, Zhang X, Yan B, Cao D. Design of Small Nanoparticles Decorated with Amphiphilic Ligands: Self-Preservation Effect and Translocation into a Plasma Membrane. ACS APPLIED MATERIALS & INTERFACES 2019; 11:23822-23831. [PMID: 31250627 DOI: 10.1021/acsami.9b03638] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Design of nanoparticles (NPs) for biomedical applications requires a thorough understanding of cascades of nano-bio interactions at different interfaces. Here, we take into account the cascading effect of NP functionalization on interactions with target cell membranes by determining coatings of biomolecules in biological media. Cell culture experiments show that NPs with more hydrophobic surfaces are heavily ingested by cells in both the A549 and HEK293 cell lines. However, before reaching the target cell, both the identity and amount of recruited biomolecules can be influenced by the pristine NPs' hydrophobicity. Dissipative particle dynamics (DPD) simulations show that hydrophobic NPs acquire coatings of more biomolecules, which may conceal the properties of the as-engineered NPs and impact the targeting specificity. Based on these results, we propose an amphiphilic ligand coating on NPs. DPD simulations reveal the design principle, following which the amphiphilic ligands first curl in solvent to reduce the surface hydrophobicity, thus suppressing the assemblage of biomolecules. Upon attaching to the membrane, the curled ligands extend and rearrange to gain contacts with lipid tails, thus dragging NPs into the membrane for translocation. Three NP-membrane interaction states are identified that are found to depend on the NP size and membrane surface tension. These results can provide useful guidelines to fabricate ligand-coated NPs for practical use in targeted drug delivery, and motivate further studies of nano-bio-interactions with more consideration of cascading effects.
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Affiliation(s)
- Yuchi Liu
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Xuejuan Liu
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Hainan Sun
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Bing Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay , Guangzhou University , Guangzhou 510006 , China
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Dapeng Cao
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
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38
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Zhu W, Kong J, Zhang J, Wang J, Li W, Wang W. Consequences of Hydrophobic Nanotube Binding on the Functional Dynamics of Signaling Protein Calmodulin. ACS OMEGA 2019; 4:10494-10501. [PMID: 31460146 PMCID: PMC6648716 DOI: 10.1021/acsomega.9b01217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
The wide applications of nanomaterials in industry and our daily life have raised growing concerns on their toxicity to human body. Increasing evidence links the cytotoxicity of nanoparticles to the disruption of cellular signaling pathways. Here, we report a computational study on the mechanisms of the cytotoxicity of carbon nanotubes (CNTs) by investigating the direct impacts of CNTs on the functional motions of calmodulin (CaM), which is one of the most important signaling proteins in a cell, and its signaling function relies on the Ca2+ binding-coupled conformational switching. Computational simulations with a coarse-grained model showed that binding of CNTs modifies the conformational equilibrium of CaM and induces the closed-to-open conformational transition, leading to the loss of its Ca2+-sensing ability. In addition, the binding of CNTs drastically increases the calcium affinity of CaM, which may disrupt the Ca2+ homeostasis in a cell. These results suggest that the binding of hydrophobic nanotubes not only inhibits the signaling function of CaM as a calcium sensor but also renders CaM to toxic species through sequestering Ca2+ from other competing calcium-binding proteins, suggesting a new physical mechanism of the cytotoxicity of nanoparticles.
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Affiliation(s)
- Wentao Zhu
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jianyang Kong
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
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39
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Ganazzoli F, Raffaini G. Classical atomistic simulations of protein adsorption on carbon nanomaterials. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Jia Z, Ma Y, Yang L, Guo C, Zhou N, Wang M, He L, Zhang Z. NiCo2O4 spinel embedded with carbon nanotubes derived from bimetallic NiCo metal-organic framework for the ultrasensitive detection of human immune deficiency virus-1 gene. Biosens Bioelectron 2019; 133:55-63. [DOI: 10.1016/j.bios.2019.03.030] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/12/2019] [Accepted: 03/17/2019] [Indexed: 01/22/2023]
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41
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Hirano A, Wada M, Tanaka T, Kataura H. Oxidative Stress of Carbon Nanotubes on Proteins Is Mediated by Metals Originating from the Catalyst Remains. ACS NANO 2019; 13:1805-1816. [PMID: 30680990 DOI: 10.1021/acsnano.8b07936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanomaterials introduced into biological systems are immediately coated by proteins in vivo. They induce oxidative stress on adsorbed proteins and hence alter the protein structures, which determines the fate pathways and biological impacts of nanomaterials. Carbon nanotubes (CNTs) have been suggested to cause protein oxidation. In this work, we discovered that CNTs induce oxidative stress on proteins in cooperation with coexisting metals originating from catalyst remains. Protein sulfhydryl groups were readily oxidized by the coexistence of CNTs and metals. Numerical simulations of the reaction demonstrated that the metals effectively mediate electron transfer between the CNTs and protein sulfhydryl groups. Thus, the coexistence of CNTs and metals, even in low concentrations, generates oxidative stress on proteins with high reaction rates. Metal catalysts used for CNT growth, in turn, catalyze the oxidation reaction of proteins. The proposed protein oxidation mechanism will advance the fundamental understanding of the biological safety and toxicity of nanomaterials synthesized using metal catalysts.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Ibaraki 305-8565 , Japan
| | - Momoyo Wada
- Nanomaterials Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Ibaraki 305-8565 , Japan
| | - Takeshi Tanaka
- Nanomaterials Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Ibaraki 305-8565 , Japan
| | - Hiromichi Kataura
- Nanomaterials Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Ibaraki 305-8565 , Japan
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42
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Taale M, Schütt F, Carey T, Marx J, Mishra YK, Stock N, Fiedler B, Torrisi F, Adelung R, Selhuber-Unkel C. Biomimetic Carbon Fiber Systems Engineering: A Modular Design Strategy To Generate Biofunctional Composites from Graphene and Carbon Nanofibers. ACS APPLIED MATERIALS & INTERFACES 2019; 11:5325-5335. [PMID: 30600988 PMCID: PMC6369718 DOI: 10.1021/acsami.8b17627] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/02/2019] [Indexed: 05/21/2023]
Abstract
Carbon-based fibrous scaffolds are highly attractive for all biomaterial applications that require electrical conductivity. It is additionally advantageous if such materials resembled the structural and biochemical features of the natural extracellular environment. Here, we show a novel modular design strategy to engineer biomimetic carbon fiber-based scaffolds. Highly porous ceramic zinc oxide (ZnO) microstructures serve as three-dimensional (3D) sacrificial templates and are infiltrated with carbon nanotubes (CNTs) or graphene dispersions. Once the CNTs and graphene coat the ZnO template, the ZnO is either removed by hydrolysis or converted into carbon by chemical vapor deposition. The resulting 3D carbon scaffolds are both hierarchically ordered and free-standing. The properties of the microfibrous scaffolds were tailored with a high porosity (up to 93%), a high Young's modulus (ca. 0.027-22 MPa), and an electrical conductivity of ca. 0.1-330 S/m, as well as different surface compositions. Cell viability, fibroblast proliferation rate and protein adsorption rate assays have shown that the generated scaffolds are biocompatible and have a high protein adsorption capacity (up to 77.32 ± 6.95 mg/cm3) so that they are able to resemble the extracellular matrix not only structurally but also biochemically. The scaffolds also allow for the successful growth and adhesion of fibroblast cells, showing that we provide a novel, highly scalable modular design strategy to generate biocompatible carbon fiber systems that mimic the extracellular matrix with the additional feature of conductivity.
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Affiliation(s)
- Mohammadreza Taale
- Biocompatible
Nanomaterials, Institute for Materials Science and Functional Nanomaterials,
Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Fabian Schütt
- Biocompatible
Nanomaterials, Institute for Materials Science and Functional Nanomaterials,
Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Tian Carey
- Cambridge
Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge CB3 0FA, U.K.
| | - Janik Marx
- Institute
of Polymer and Composites, Hamburg University
of Technology, Denickestraße
15, D-21073 Hamburg, Germany
| | - Yogendra Kumar Mishra
- Biocompatible
Nanomaterials, Institute for Materials Science and Functional Nanomaterials,
Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Norbert Stock
- Institute
of Inorganic Chemistry, Kiel University, Max-Eyth Straße 2, D-24118 Kiel, Germany
| | - Bodo Fiedler
- Institute
of Polymer and Composites, Hamburg University
of Technology, Denickestraße
15, D-21073 Hamburg, Germany
| | - Felice Torrisi
- Cambridge
Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge CB3 0FA, U.K.
| | - Rainer Adelung
- Biocompatible
Nanomaterials, Institute for Materials Science and Functional Nanomaterials,
Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Christine Selhuber-Unkel
- Biocompatible
Nanomaterials, Institute for Materials Science and Functional Nanomaterials,
Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
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43
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Butnaru D, Chapman J. The impact of self-replicating proteins on inflammation, autoimmunity and neurodegeneration-An untraveled path. Autoimmun Rev 2019; 18:231-240. [PMID: 30639644 DOI: 10.1016/j.autrev.2018.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 02/08/2023]
Abstract
The central nervous system (CNS) in neurodegenerative diseases is a battlefield in which microglia fight a highly atypical battle. During the inflammatory process microglia themselves become dysfunctional and even with all the available immune arsenal including cytokine or/and antibody production, the battle is eventually lost. A closer look into the picture will reveal the fact that this is mainly due to the atypical characteristics of the infectious agent. The supramolecular assemblies of misfolded proteins carry unique features not encountered in any of the common pathogens. Through misfolding, proteins undergo conformational changes which make them become immunogenic, neurotoxic and highly infective. The immunogenicity appears to be triggered by the exposure of previously hidden hydrophobic portions in proteins which act as damage-associated molecular patters (DAMPs) for the immune system. The neurotoxicity and infectivity are promoted by the small oligomeric forms of misfolded proteins/peptides. Oligomers adopt conformations such as tubular-like, beta-barrel-like, etc., that penetrate cell membranes through their hydrophobic surfaces, thus destabilizing ionic homeostasis. At the same time, oligomers act as a seed for protein misfolding through a prion/prion-like mechanism. Here, we propose the hypothesis that oligomers have catalytic surfaces and exercise their capacity to infect native proteins through specific characteristics such as hydrophobic, electrostatic and π-π stacking interactions as well as the specific surface area (SSA), surface curvature and surface chemistry of their nanoscale supramolecular assemblies. All these are the key elements for prion/prion-like mechanism of self-replication and disease spreading within the CNS. Thus, understanding the mechanism of prion's templating activity may help us in the prevention and development of novel therapeutic strategies for neurodegenerative diseases.
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Affiliation(s)
- Dana Butnaru
- The Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel.
| | - Joab Chapman
- Sheba Medical Center, Israel; Robert and Martha Harden Chair in Mental and Neurological Diseases, Sackler Faculty of Medicine, Tel Aviv University, Israel
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Strojny B, Sawosz E, Grodzik M, Jaworski S, Szczepaniak J, Sosnowska M, Wierzbicki M, Kutwin M, Orlińska S, Chwalibog A. Nanostructures of diamond, graphene oxide and graphite inhibit CYP1A2, CYP2D6 and CYP3A4 enzymes and downregulate their genes in liver cells. Int J Nanomedicine 2018; 13:8561-8575. [PMID: 30587978 PMCID: PMC6300366 DOI: 10.2147/ijn.s188997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION AND OBJECTIVE Currently, carbon nanostructures are vastly explored materials with potential for future employment in biomedicine. The possibility of employment of diamond nanoparticles (DN), graphene oxide (GO) or graphite nanoparticles (GN) for in vivo applications raises a question of their safety. Even though they do not induce a direct toxic effect, due to their unique properties, they can still interact with molecular pathways. The objective of this study was to assess if DN, GO and GN affect three isoforms of cytochrome P450 (CYP) enzymes, namely, CYP1A2, CYP2D6 and CYP3A4, expressed in the liver. METHODS Dose-dependent effect of the DN, GO and GN nanostructures on the catalytic activity of CYPs was examined using microsome-based model. Cytotoxicity of DN, GO and GN, as well as the influence of the nanostructures on mRNA expression of CYP genes and CYP-associated receptor genes were studied in vitro using HepG2 and HepaRG cell lines. RESULTS All three nanostructures interacted with the CYP enzymes and inhibited their catalytic activity in microsomal-based models. CYP gene expression at the mRNA level was also downregulated in HepG2 and HepaRG cell lines. Among the three nanostructures, GO showed the most significant influence on the enzymes, while DN was the most inert. CONCLUSION Our findings revealed that DN, GO and GN might interfere with xenobiotic and drug metabolism in the liver by interactions with CYP isoenzymes responsible for the process. Such results should be considered if DN, GO and GN are used in medical applications.
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Affiliation(s)
- Barbara Strojny
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ewa Sawosz
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Marta Grodzik
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Sławomir Jaworski
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Jarosław Szczepaniak
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Malwina Sosnowska
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Mateusz Wierzbicki
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Marta Kutwin
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Sylwia Orlińska
- Division of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - André Chwalibog
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark,
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Ebrahim-Habibi MB, Ghobeh M, Aghakhani Mahyari F, Rafii-Tabar H, Sasanpour P. Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study. J Mol Graph Model 2018; 87:257-267. [PMID: 30594774 DOI: 10.1016/j.jmgm.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. METHODS Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. RESULTS Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch. CONCLUSION Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.
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Affiliation(s)
- Mohammad-Bagher Ebrahim-Habibi
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Ghobeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Pezhman Sasanpour
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; School of Nanoscience, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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Mo Y, Brahmachari S, Lei J, Gilead S, Tang Y, Gazit E, Wei G. The Inhibitory Effect of Hydroxylated Carbon Nanotubes on the Aggregation of Human Islet Amyloid Polypeptide Revealed by a Combined Computational and Experimental Study. ACS Chem Neurosci 2018; 9:2741-2752. [PMID: 29986579 DOI: 10.1021/acschemneuro.8b00166] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Fibrillar deposits formed by the aggregation of the human islet amyloid polypeptide (hIAPP) are the major pathological hallmark of type 2 diabetes mellitus (T2DM). Inhibiting the aggregation of hIAPP is considered the primary therapeutic strategy for the treatment of T2DM. Hydroxylated carbon nanoparticles have received great attention in impeding amyloid protein fibrillation owing to their reduced cytotoxicity compared to the pristine ones. In this study, we investigated the influence of hydroxylated single-walled carbon nanotubes (SWCNT-OHs) on the first step of hIAPP aggregation: dimerization by performing explicit solvent replica exchange molecular dynamics (REMD) simulations. Extensive REMD simulations demonstrate that SWCNT-OHs can dramatically inhibit interpeptide β-sheet formation and completely suppress the previously reported β-hairpin amyloidogenic precursor of hIAPP. On the basis of our simulation results, we proposed that SWCNT-OH can hinder hIAPP fibrillation. This was further confirmed by our systematic turbidity measurements, thioflavin T fluorescence, circular dichroism (CD), transmission electron microscope (TEM), and atomic force microscopy (AFM) experiments. Detailed analyses of hIAPP-SWCNT-OH interactions reveal that hydrogen bonding, van der Waals, and π-stacking interactions between hIAPP and SWCNT-OH significantly weaken the inter- and intrapeptide interactions that are crucial for β-sheet formation. Our collective computational and experimental data reveal not only the inhibitory effect but also the inhibitory mechanism of SWCNT-OH against hIAPP aggregation, thus providing new clues for the development of future drug candidates against T2DM.
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Affiliation(s)
- Yuxiang Mo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
- College of Physical Science and Technology, Guangxi Normal University, 15 Yucai Road, Guilin 541004, People’s Republic of China
| | - Sayanti Brahmachari
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Sharon Gilead
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yiming Tang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures, and Department of Physics, Fudan University, Shanghai 200433, People’s Republic of China
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Wang C, Jiang Y, Zhang M, Fei X, Gu Y. Novel fluorescent antifolates that target folate receptors α and β: Molecular dynamics and density functional theory study. J Mol Graph Model 2018; 85:40-47. [PMID: 30055477 DOI: 10.1016/j.jmgm.2018.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/14/2018] [Accepted: 07/22/2018] [Indexed: 01/19/2023]
Abstract
Nine novel fluorescent antifolates, 1-9, were designed and docked with FRα and FRβ. The binding energies of the bound complexes were determined by molecular docking and MM-PBSA studies. The structural properties of the complexes FR-FOL, FR-7, FR-8 and FR-9 were analyzed in detail via molecular docking and molecular dynamics studies. We further calculated the root mean square displacement and root mean square fluctuation of the bound complexes using molecular dynamics simulations. Since compounds 7, 8 and 9 are promising candidate in distinguishing FRα from FRβ, the hydrogen bond properties of complexes FRα-7, FRα-8 and FRα-9 were studied by a dispersion complemented density functional tight-binding method. The purpose of this study is to provide a rationale for the design of novel fluorescent antifolates targeted with FRα and FRβ.
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Affiliation(s)
- Cuihong Wang
- School of Science, TianJin ChengJian University, Tianjin, China.
| | - Yue Jiang
- School of Science, TianJin ChengJian University, Tianjin, China
| | - Meiling Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Xuening Fei
- School of Science, TianJin ChengJian University, Tianjin, China.
| | - Yingchun Gu
- School of Science, TianJin ChengJian University, Tianjin, China
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48
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The potential impact of carboxylic-functionalized multi-walled carbon nanotubes on trypsin: A Comprehensive spectroscopic and molecular dynamics simulation study. PLoS One 2018; 13:e0198519. [PMID: 29856868 PMCID: PMC5983559 DOI: 10.1371/journal.pone.0198519] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/21/2018] [Indexed: 01/03/2023] Open
Abstract
In this study, we report a detailed experimental, binding free energy calculation and molecular dynamics (MD) simulation investigation of the interactions of carboxylic-functionalized multi-walled carbon nanotubes (COOH-f-MWCNTs) with porcine trypsin (pTry). The enzyme exhibits decreased thermostability at 330K in the presence of COOH-f-MWCNTs. Furthermore, the activity of pTry also decreases in the presence of COOH-f-MWCNTs. The restricted diffusion of the substrate to the active site of the enzyme was observed in the experiment. The MD simulation analysis suggested that this could be because of the blocking of the S1 pocket of pTry, which plays a vital role in the substrate selectivity. The intrinsic fluorescence of pTry is quenched with increase in the COOH-f-MWCNTs concentration. Circular dichroism (CD) and UV–visible absorption spectroscopies indicate the ability of COOH-f-MWCNTs to experience conformational change in the native structure of the enzyme. The binding free energy calculations also show that electrostatics, π-cation, and π-π stacking interactions play important roles in the binding of the carboxylated CNTs with pTry. The MD simulation results demonstrated that the carboxylated CNTs adsorb to the enzyme stronger than the CNT without the–COOH groups. Our observations can provide an example of the nanoscale toxicity of COOH-f-MWCNTs for proteins, which is a critical issue for in vivo application of COOH-f-MWCNTs.
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Advances in surface-coated single-walled carbon nanotubes as near-infrared photoluminescence emitters for single-particle tracking applications in biological environments. Polym J 2018. [DOI: 10.1038/s41428-018-0052-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Wang C, Jiang Y, Fei X, Gu Y. Design and interaction mechanism of ligand targeted with folate receptor α and β. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- C. Wang
- School of Science; TianJin ChengJian University; Tianjin China
| | - Y. Jiang
- School of Science; TianJin ChengJian University; Tianjin China
| | - X. Fei
- School of Science; TianJin ChengJian University; Tianjin China
| | - Y. Gu
- School of Science; TianJin ChengJian University; Tianjin China
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