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Du J, Yang C, Ma X, Li Q. Insights into the conformation changes of SARS-CoV-2 spike receptor-binding domain on graphene. APPLIED SURFACE SCIENCE 2022; 578:151934. [PMID: 34866721 PMCID: PMC8627288 DOI: 10.1016/j.apsusc.2021.151934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/24/2021] [Accepted: 11/14/2021] [Indexed: 05/13/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread in the world, causing more than two million deaths and seriously threatening human life. Effective protection measures are important to prevent the infection and spreading of the virus. To explore the effects of graphene on the virus adsorption and its biological properties, the adsorption process of the receptor binding domain (RBD) of SARS-CoV-2 on graphene has been investigated by molecular dynamics simulations in this paper. The results show that RBD can be quickly adsorbed onto the surface of graphene due to π - π stacking and hydrophobic interactions. Residue PHE486 with benzene ring has stronger adsorption force and the maximum contact area with graphene. Graphene significantly affects the secondary structure of RBD area, especially on the three key sites of binding with human ACE2, GLY476, PHE486 and ASN487. The binding free energy of RBD and graphene shows that the adsorption is irreversible. Undoubtedly, these changes will inevitably affect the pathogenicity of the virus. Therefore, this study provides a theoretical basis for the application of graphene in the protection of SARS-CoV-2, and also provides a reference for the potential application of graphene in the biomedical field.
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Affiliation(s)
- Jianbin Du
- College of Science, Langfang Normal University, Langfang 065000, China
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Chunmei Yang
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xiangyun Ma
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Qifeng Li
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
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2
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Wang J, Dong H, Leng T, Yu Y, Li Y. Turning the structure of the Aβ 42 peptide by different functionalized carbon nanotubes: a molecular dynamics simulation study. Phys Chem Chem Phys 2022; 24:4270-4279. [PMID: 35107452 DOI: 10.1039/d1cp04278e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functionalized carbon nanotubes (CNTs) can inhibit the self-assembly of amyloid-beta (Aβ) peptides. Under abnormal conditions, the structure of the Aβ peptides undergoes a fundamental transformation, and this transformation will induce conformational conversions of other polymerized Aβ peptides. Here, we explore the interactions between different functionalized CNTs and Aβ42 peptides by molecular dynamics simulations. Our results show that compared to the original CNTs, the highly functionalized CNTs induce different adsorption patterns of the peptides. This adsorption pattern destroys the α-helix structure and increases the β-turn and random coil content significantly. The hydrogen bonds formed by the peptide and water molecules or CNTs further reveal the reasons for the structural transformation of the peptide. Due to electrostatic interactions and π-π stacking interactions, some amino acids (such as Phe4, Lys16, Phe20, and Lys28) are tightly fixed on the surfaces, and other amino acids move around these amino acids to accelerate the unfolding and denaturation of the peptide. Our research shows that functionalized CNTs have excellent potential to inhibit the abnormal aggregation of Aβ42 peptides. Our research also provides theoretical guidance in the design and synthesis of carbon nanomedicines for protein conformation diseases.
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Affiliation(s)
- Jiawen Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
| | - Huilong Dong
- School of Materials Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Tianle Leng
- Dougherty Valley High School, 10550 Albion Rd, San Ramon, CA 94582, USA
| | - Yi Yu
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China. .,Macao Institute of Materials Science and Engineering, Macau University of Science and Technology, Taipa 999078, Macau SAR, China
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Zhao W, Jiang L, Wang W, Sang J, Sun Q, Dong Q, Li L, Lu F, Liu F. Design of carboxylated single-walled carbon nanotubes as highly efficient inhibitors against Aβ40 fibrillation based on the HyBER mechanism. J Mater Chem B 2021; 9:6902-6914. [PMID: 34612337 DOI: 10.1039/d1tb00920f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Misfolding and the subsequent self-assembly of amyloid-β protein (Aβ) is very important in the occurrence of Alzheimer's disease (AD). Thus, inhibition of Aβ aggregation is currently an effective method to alleviate and treat AD. Herein, a carboxylated single-walled carbon nanotube (SWCNT-COOH) was rationally designed based on the hydrophobic binding-electrostatic repulsion (HyBER) mechanism. The inhibitory effect of SWCNT-COOH on Aβ fibrillogenesis was first studied. Based on the results of thioflavin T fluorescence and atomic force microscopy imaging assays, it was shown that SWCNT-COOH can not only effectively inhibit Aβ aggregation, but also depolymerize the mature fibrils of Aβ. In addition, its inhibitory action will be affected by the content of carboxyl groups. Moreover, the influence of SWCNT-COOH on cytotoxicity induced by Aβ was investigated by the MTT method. It was found that SWCNT-COOH can produce an anti-Aβ neuroprotective effect in vitro. Molecular dynamics simulations showed that SWCNT-COOH significantly destroyed the overall and internal structural stability of an Aβ40 trimer. Moreover, SWCNT-COOH interacted strongly with the N-terminal region, turn region and C-terminal region of the Aβ40 trimer via hydrogen bonds, salt bridges and π-π interactions, which triggered a large structural disturbance of the Aβ40 trimer, reduced the β-sheet content of the Aβ40 trimer and led to more disorder in these regions. All the above data not only reveal the suppressive effect of SWCNT-COOH on Aβ aggregation, but also reveal its inhibitory mechanism, which provides a useful clue to exploit anti-Aβ drugs in the future.
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Affiliation(s)
- Wenping Zhao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
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Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem 2021; 275:106609. [PMID: 33975078 DOI: 10.1016/j.bpc.2021.106609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/27/2022]
Abstract
Understanding how antibodies adsorb on solid surfaces is essential for developing effective approaches to control this process. In this study, passive adsorptions on the hydrophobic solid surface of a polystyrene microparticle (MP) of two highly similar IgG1 κ-type monoclonal antibodies (mAbs), rituximab, and trastuzumab, were examined in the presence of Hofmeister salts. Except of kosmotropic salts, the screening of electrostatic interactions using salts reduces the passive adsorption of mAbs on MP. To better understand the ion-specific adsorption process, salt-dependent Langmuir isotherm parameters were obtained and correlated for two mAbs. We find that while their maximum adsorption capacities to MPs are highly correlated (r > 0.9), the salt-dependent profiles of adsorption binding constants, Kobs, differ substantially. For rituximab, Kobs increases >10-fold in an ion-specific manner; for trastuzumab, Kobs remains constant. We conclude that even minor sequence variations among the mAbs can affect the adsorption, as well as the molecular forces attracting proteins to a solid surface. This difference might originate from the heterogeneous orientation of the adsorbed mAbs.
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Affiliation(s)
- Veronika Džupponová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University, Jesenna 5, 040 01 Košice, Slovakia
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Trieda SNP 1, 040 11 Košice, Slovakia.
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Ding HM, Ma YQ. Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity. NANOSCALE HORIZONS 2018; 3:6-27. [PMID: 32254106 DOI: 10.1039/c7nh00138j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.
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Affiliation(s)
- Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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Lin D, Qi R, Li S, He R, Li P, Wei G, Yang X. Interaction Dynamics in Inhibiting the Aggregation of Aβ Peptides by SWCNTs: A Combined Experimental and Coarse-Grained Molecular Dynamic Simulation Study. ACS Chem Neurosci 2016; 7:1232-40. [PMID: 27441457 DOI: 10.1021/acschemneuro.6b00101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The aggregation of amyloid-β peptides (Aβ) is considered as the main possible cause of Alzheimer's disease (AD). How to suppress the formation of toxic Aβ aggregates has been an intensive concern over the past several decades. Increasing evidence shows that whether carbon nanomaterials can suppress or promote the aggregation depends on their physicochemical properties. However, their interaction dynamics remains elusive as amyloid fibrillation is a complex multistep process. In this paper, we utilized atomic force microscopy (AFM), electrostatic force microscopy (EFM), ThT/fluorescence spectroscopy, and cell viability measurements, combined with coarse-grained molecular dynamic (MD) simulations to study the dynamic interaction of full length Aβ with single-walled carbon nanotubes (SWCNT). At the single SWCNTs scale, it is found that the presence of SWCNTs would result in rapid and spontaneous adsorption of Aβ1-40 peptides on their surface and stacking into nonfibrillar aggregates with reduced toxicity, which plays an important role in inhibiting the formation of toxic oligomers and mature fibrils. Our results provide new clues for studying the interaction in amyloid/SWCNTs system as well as for seeking amyloidosis inhibitors with carbon nanomaterials.
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Affiliation(s)
- Dongdong Lin
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Ruxi Qi
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Shujie Li
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Ruoyu He
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Pei Li
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
| | - Xinju Yang
- State Key Laboratory of Surface
Physics and Key Laboratory for Computational Physical, Fudan University, Shanghai 200433, China
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Jana AK, Tiwari MK, Vanka K, Sengupta N. Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures. Phys Chem Chem Phys 2016; 18:5910-24. [DOI: 10.1039/c5cp04675k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Underlying causes of the differential polypeptide interactions on carbon nanosurfaces of varying curvatures emerge from a synchronized computational study.
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Affiliation(s)
- Asis K. Jana
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | | | - Kumar Vanka
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Neelanjana Sengupta
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
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Jana AK, Sengupta N. Aβ self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response. SOFT MATTER 2015; 11:269-279. [PMID: 25407676 DOI: 10.1039/c4sm01845a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Treatment of Alzheimer's disease (AD) is impeded by the lack of effective early diagnostic methods. Small, soluble Aβ globulomers play a major role in AD neurotoxicity, and detecting their presence in aqueous fluids could lead to suitable sensors. We evaluate the adsorption behavior of small Aβ oligomers on the surface of a single walled carbon nanotube of high curvature. While the intrinsic self-assembly propensity of Aβ is markedly hindered by adsorption, the oligomeric units show high degrees of surface immobilization. Immobilized complexes are capable of oligomeric growth, but with a shifted monomer-oligomer equilibrium compared to the free states. In the presence of an ionic solution and suitable external electric fields, magnitudes of the current blockades are found to be sensitive to the oligomeric number of the adsorbed complex. However, this sensitivity gradually diminishes with increasing oligomeric size. The results provide a proof-of-concept basis for further investigations in the design of sensors for detecting the toxic small oligomers of Aβ.
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Affiliation(s)
- Asis K Jana
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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Xie L, Lin D, Luo Y, Li H, Yang X, Wei G. Effects of hydroxylated carbon nanotubes on the aggregation of Aβ16-22 peptides: a combined simulation and experimental study. Biophys J 2014; 107:1930-1938. [PMID: 25418174 PMCID: PMC4213673 DOI: 10.1016/j.bpj.2014.08.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/27/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
The pathogenesis of Alzheimer's disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with ?-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ16-22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ16-22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ16-22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ16-22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ16-22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ16-22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.
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Affiliation(s)
- Luogang Xie
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Dongdong Lin
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Yin Luo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Huiyu Li
- Department of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, China
| | - Xinju Yang
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China.
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