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Forte G, La Mendola D, Satriano C. The Hybrid Nano-Biointerface between Proteins/Peptides and Two-Dimensional Nanomaterials. Molecules 2023; 28:7064. [PMID: 37894543 PMCID: PMC10609159 DOI: 10.3390/molecules28207064] [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: 08/17/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
In typical protein-nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the layer formed when biomolecules, especially proteins and peptides, face two-dimensional (2D) nanomaterials, to provide an overview of the state-of-the-art knowledge and the current challenges concerning the biomolecule coronas and, in general, the 2D nano-biointerface established when peptides and proteins interact with the nanosheet surface. Specifically, this review includes both experimental and simulation studies, including some recent machine learning results of a wide range of nanomaterial and peptide/protein systems.
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Affiliation(s)
- Giuseppe Forte
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy;
| | - Diego La Mendola
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy;
| | - Cristina Satriano
- NanoHybrid Biointerfaces Laboratory (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125 Catania, Italy
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2
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Lu Q, Yu H, Zhao T, Zhu G, Li X. Nanoparticles with transformable physicochemical properties for overcoming biological barriers. NANOSCALE 2023; 15:13202-13223. [PMID: 37526946 DOI: 10.1039/d3nr01332d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
In recent years, tremendous progress has been made in the development of nanomedicines for advanced therapeutics, yet their unsatisfactory targeting ability hinders the further application of nanomedicines. Nanomaterials undergo a series of processes, from intravenous injection to precise delivery at target sites. Each process faces different or even contradictory requirements for nanoparticles to pass through biological barriers. To overcome biological barriers, researchers have been developing nanomedicines with transformable physicochemical properties in recent years. Physicochemical transformability enables nanomedicines to responsively switch their physicochemical properties, including size, shape, surface charge, etc., thus enabling them to cross a series of biological barriers and achieve maximum delivery efficiency. In this review, we summarize recent developments in nanomedicines with transformable physicochemical properties. First, the biological dilemmas faced by nanomedicines are analyzed. Furthermore, the design and synthesis of nanomaterials with transformable physicochemical properties in terms of size, charge, and shape are summarized. Other switchable physicochemical parameters such as mobility, roughness and mechanical properties, which have been sought after most recently, are also discussed. Finally, the prospects and challenges for nanomedicines with transformable physicochemical properties are highlighted.
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Affiliation(s)
- Qianqian Lu
- Department of Chemistry, Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), Fudan University, Shanghai 200433, P. R. China.
| | - Hongyue Yu
- Department of Chemistry, Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), Fudan University, Shanghai 200433, P. R. China.
| | - Tiancong Zhao
- Department of Chemistry, Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), Fudan University, Shanghai 200433, P. R. China.
| | - Guanjia Zhu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, P. R. China.
| | - Xiaomin Li
- Department of Chemistry, Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), Fudan University, Shanghai 200433, P. R. China.
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3
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Chen Y, Zhu F, Leng J, Ying T, Jiang JW, Zhou Q, Chang T, Guo W, Gao H. Fluctuotaxis: Nanoscale directional motion away from regions of fluctuation. Proc Natl Acad Sci U S A 2023; 120:e2220500120. [PMID: 37487105 PMCID: PMC10401016 DOI: 10.1073/pnas.2220500120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/27/2023] [Indexed: 07/26/2023] Open
Abstract
Regulating the motion of nanoscale objects on a solid surface is vital for a broad range of technologies such as nanotechnology, biotechnology, and mechanotechnology. In spite of impressive advances achieved in the field, there is still a lack of a robust mechanism which can operate under a wide range of situations and in a controllable manner. Here, we report a mechanism capable of controllably driving directed motion of any nanoobjects (e.g., nanoparticles, biomolecules, etc.) in both solid and liquid forms. We show via molecular dynamics simulations that a nanoobject would move preferentially away from the fluctuating region of an underlying substrate, a phenomenon termed fluctuotaxis-for which the driving force originates from the difference in atomic fluctuations of the substrate behind and ahead of the object. In particular, we find that the driving force can depend quadratically on both the amplitude and frequency of the substrate and can thus be tuned flexibly. The proposed driving mechanism provides a robust and controllable way for nanoscale mass delivery and has potential in various applications including nanomotors, molecular machines, etc.
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Affiliation(s)
- Yang Chen
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Fangyan Zhu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jiantao Leng
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tianquan Ying
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jin-Wu Jiang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
| | - Quan Zhou
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tienchong Chang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
- Shanghai Institute of Aircraft Mechanics and Control, Tongji University, Shanghai200092, China
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, Institute of Nanoscience of Nanjing University of Aeronautics and Astronautics, Nanjing210016, China
| | - Huajian Gao
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
- Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore138632, Singapore
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4
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Li J, Yang F, Liu D, Han S, Li J, Sui G. Graphene composite paper synergized with micro/nanocellulose-fiber and silk fibroin for flexible strain sensor. Int J Biol Macromol 2023; 240:124439. [PMID: 37062378 DOI: 10.1016/j.ijbiomac.2023.124439] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/18/2023]
Abstract
The fabrication of uniform and strong graphene-based conductive paper is challenging due to easy aggregation and poor film formability of graphene. Herein, on the basis of good dispersing effect of nanocellulose, high content graphene (50 wt%) composite paper with micro/nanocellulose fibers and silk fibroin (SF) was manufactured via simple casting method. The synergistic effects of cellulose microfibers (CMFs), cellulose nanofibers (CNFs) and SF result in the paper with ideal combination of flexibility, electrical conductivity and mechanical strength, where CNFs, CMFs and SF act as dispersing and film forming for GNPs, dimensional stability, and interfacial binding agents, respectively. Extraordinarily, by adding SF, graphene nanosheets are tightly coated on the surface of CMFs. The composite paper shows a tensile strength of 49.29 MPa, surface resistance of 39.0-42.1 Ω and good joints bend sensing performance. Additionally, it is found that CMFs can hinder the micro-cracks from propagating during the cyclic elbow bending test. The graphene-based conductive paper is helpful for the development of smart clothing wearable biosensing devices.
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Affiliation(s)
- Jun Li
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China; School of Materials Science and Engineering, University of Science and Technology of China, Shenyang 110016, China
| | - Fei Yang
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China; School of Materials Science and Engineering, University of Science and Technology of China, Shenyang 110016, China
| | - Dongyan Liu
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Sensen Han
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China; School of Materials Science and Engineering, University of Science and Technology of China, Shenyang 110016, China
| | - Junsheng Li
- Engineering Center of National New Raw Material Base Construction of Liaoning Province, Shenyang 110031, China
| | - Guoxin Sui
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China.
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Mousanezhad S, Davoodi J. Mechanical loading of graphene quantum dots on
Staphylococcus aureus
surface protein G: A molecular dynamics study. Biopolymers 2022; 113:e23526. [DOI: 10.1002/bip.23526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | - Jamal Davoodi
- Department of Physics University of Zanjan Zanjan Iran
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Benková Z, Cordeiro MNDS. Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene. MATERIALS TODAY. CHEMISTRY 2021; 22:100572. [PMID: 34485782 PMCID: PMC8405511 DOI: 10.1016/j.mtchem.2021.100572] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.
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Affiliation(s)
- Z Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - M N D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Rua Do Campo Alegre 687, 4168-007 Porto, Portugal
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7
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Liu Z, Wan X, Wang ZL, Li L. Electroactive Biomaterials and Systems for Cell Fate Determination and Tissue Regeneration: Design and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007429. [PMID: 34117803 DOI: 10.1002/adma.202007429] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/19/2020] [Indexed: 06/12/2023]
Abstract
During natural tissue regeneration, tissue microenvironment and stem cell niche including cell-cell interaction, soluble factors, and extracellular matrix (ECM) provide a train of biochemical and biophysical cues for modulation of cell behaviors and tissue functions. Design of functional biomaterials to mimic the tissue/cell microenvironment have great potentials for tissue regeneration applications. Recently, electroactive biomaterials have drawn increasing attentions not only as scaffolds for cell adhesion and structural support, but also as modulators to regulate cell/tissue behaviors and function, especially for electrically excitable cells and tissues. More importantly, electrostimulation can further modulate a myriad of biological processes, from cell cycle, migration, proliferation and differentiation to neural conduction, muscle contraction, embryogenesis, and tissue regeneration. In this review, endogenous bioelectricity and piezoelectricity are introduced. Then, design rationale of electroactive biomaterials is discussed for imitating dynamic cell microenvironment, as well as their mediated electrostimulation and the applying pathways. Recent advances in electroactive biomaterials are systematically overviewed for modulation of stem cell fate and tissue regeneration, mainly including nerve regeneration, bone tissue engineering, and cardiac tissue engineering. Finally, the significance for simulating the native tissue microenvironment is emphasized and the open challenges and future perspectives of electroactive biomaterials are concluded.
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Affiliation(s)
- Zhirong Liu
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xingyi Wan
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhong Lin Wang
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0245, USA
| | - Linlin Li
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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8
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Liu R, Zhai H, Meng Y, Zhu M, Wen T, Jin N. Adsorption Behaviors of Typical Proteins on BP, GR, and C 2N Surfaces. J Chem Inf Model 2021; 61:1300-1306. [PMID: 33666087 DOI: 10.1021/acs.jcim.0c01036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biotoxicity of nanomaterials is very important for the application of nanomaterials in biomedical systems. In this study, proteins with varying secondary structures (α-helices, β-sheets, and mixed α/β structures) were employed to investigate the biological properties of three representative two-dimensional (2D) nanomaterials; these nanomaterials consisted of black phosphorus (BP), graphene (GR), and nitrogenized graphene (C2N) and were studied using molecular dynamics simulations. The results showed that the α-helix motif underwent a slight structural change on the BP surface and little structural change on the C2N surface. In contrast, the structure of the β-sheet motif remained fairly intact on both the BP and C2N surfaces. The α-helix and β-sheet motifs were able to freely migrate on the BP surface, but they were anchored to the C2N surface. In contrast to BP and C2N, GR severely disrupted the structures of the α-helix and β-sheet motifs. BBA protein with mixed α/β structures adsorbed on the BP and C2N surfaces and exhibited biological behaviors that were consistent with those of the α-helix and β-sheet motifs. In summary, C2N may possess better biocompatibility than BP and GR and is expected to have applications in the biomedical field. This study not only comprehensively evaluated the biological characteristics of nanomaterials but also provided a theoretical strategy to explore and distinguish the surface characteristics of nanomaterials.
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Affiliation(s)
- Ruirui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Honglin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Yajie Meng
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Min Zhu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Tao Wen
- Gansu Computing Center, Lanzhou 730030, China
| | - Nengzhi Jin
- Gansu Computing Center, Lanzhou 730030, China
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Sridharan S, Nagarajan SK, Venugopal K, Venkatasubbu GD. Time-dependent conformational analysis of ALK5-lumican complex in presence of graphene and graphene oxide employing molecular dynamics and MMPBSA calculation. J Biomol Struct Dyn 2021; 40:5932-5955. [PMID: 33507126 DOI: 10.1080/07391102.2021.1876772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Lumican, an extracellular matrix protein avails wound healing by binding to ALK5 membrane receptor (TGF-beta receptor I). Their interaction enables epithelialization and substantiates rejuvenation of injured tissue. To enrich permanence of ALK5-lumican interaction, we employed graphene and graphene oxide co-factors. Herein, this study explicates concomitancy of graphene and graphene oxide with ALK5-lumican. We performed an in silico approach involving molecular modelling, molecular docking, molecular dynamics for 200 ns, DSSP analysis and MMPBSA calculations. Results of molecular dynamics indicate cofactors influential in altering bioactive site of lumican than ALK5. Similarly, MMPBSA calculations unveiled binding energy of apoenzyme as -108.09 kcal/mol, holoenzyme (G) as -79.20 kcal/mol and holoenzyme (GO) as -114.33 kcal/mol. This concludes graphene oxide lucrative in enhancing binding energy of ALK5-lumican in holoenzyme (GO) via coil formation of Lum C13 domain. In contrast, graphene reduced binding energy of ALK5-lumican in holoenzyme (G) modifying Lum C13 into beta sheets. MMPBSA residual contribution analysis of Lum C13 residues revealed binding energy of -13.9 kcal/mol for apoenzyme, -6.8 kcal/mol for holoenzyme (G) and -19.5 kcal/mol for holoenzyme (GO). This supports coil formation propitious for better ALK5-Lum interaction. Highest SASA energy of -21.05 kcal/mol of holoenzyme (G) assures graphene reasonable for improved ALK5-lumican hydrophobicity. As per the motive of the study, graphene oxide enriches permanence of ALK5-lumican. This provides counsel for plausible exploitation of lumican and graphene oxide as targeted/nano drug delivery system to reinstate acute wounds, chronic wounds, corneal wounds, hypertrophic scars and keloids in near future. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sindhiya Sridharan
- Department of Nanotechnology, SRM Institute of Science and Technology, Chengalpattu, Tamil Nadu, India
| | - Santhosh Kumar Nagarajan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu, Tamil Nadu, India
| | - Kathirvel Venugopal
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu, Tamil Nadu, India
| | - G Devanand Venkatasubbu
- Department of Nanotechnology, SRM Institute of Science and Technology, Chengalpattu, Tamil Nadu, India
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10
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Kang N, Hua J, Gao L, Zhang B, Pang J. The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions. MATERIALS (BASEL, SWITZERLAND) 2021; 14:608. [PMID: 33525699 PMCID: PMC7865974 DOI: 10.3390/ma14030608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/30/2022]
Abstract
Whey protein isolate (WPI) fibrils were prepared using an acid hydrolysis induction process. Carbon nanotubes (CNTs) and carbon nano-onions (CNOs) were made via the catalytic chemical vapor deposition (CVD) of methane. WPI fibril-CNTs and WPI fibril-CNOs were prepared via hydrothermal synthesis at 80 °C. The composites were characterized by SEM, TEM, FTIR, XRD, Raman, and TG analyses. The interplay between WPI fibrils and CNTs and CNOs were studied. The WPI fibrils with CNTs and CNOs formed uniform gels and films. CNTs and CNOs were highly dispersed in the gels. Hydrogels of WPI fibrils with CNTs (or CNOs) could be new materials with applications in medicine or other fields. The CNTs and CNOs shortened the WPI fibrils, which might have important research value for curing fibrosis diseases such as Parkinson's and Alzheimer's diseases. The FTIR revealed that CNTs and CNOs both had interactions with WPI fibrils. The XRD analysis suggested that most of the CNTs were wrapped in WPI fibrils, while CNOs were partially wrapped. This helped to increase the biocompatibility and reduce the cytotoxicity of CNTs and CNOs. HR-TEM and Raman spectroscopy studies showed that the graphitization level of CNTs was higher than for CNOs. After hybridization with WPI fibrils, more defects were created in CNTs, but some original defects were dismissed in CNOs. The TG results indicated that a new phase of WPI fibril-CNTs or CNOs was formed.
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Affiliation(s)
- Ning Kang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China;
- Taiyuan Customs District, Taiyuan 030006, China;
| | - Jin Hua
- Taiyuan Customs District, Taiyuan 030006, China;
| | - Lizhen Gao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China;
| | - Bin Zhang
- Key Laboratory of Coal Science, Technology of the Ministry of Education, Taiyuan University of Technology, Taiyuan 030024, China
| | - Jiewen Pang
- College of Environment and Safety, Taiyuan University of Science and Technology, Taiyuan 030024, China;
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11
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Rissanou AN, Keliri A, Arnittali M, Harmandaris V. Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations. Phys Chem Chem Phys 2021; 22:27645-27657. [PMID: 33283818 DOI: 10.1039/d0cp03671d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.
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Affiliation(s)
- Anastassia N Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
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Zhang C, Li X, Wang Z, Huang X, Ge Z, Hu B. Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications. J Phys Chem B 2020; 124:684-694. [PMID: 31880460 DOI: 10.1021/acs.jpcb.9b10192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.
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Affiliation(s)
- Chi Zhang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xiaoyi Li
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zichen Wang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Xuqi Huang
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhenpeng Ge
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Benfeng Hu
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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Srivastava R. Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study. RSC Adv 2020; 10:38654-38662. [PMID: 35517564 PMCID: PMC9057264 DOI: 10.1039/d0ra07961h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors. We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.![]()
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad
- India
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14
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Rostampour Ghareghozloo E, Mahdavimehr M, Meratan AA, Nikfarjam N, Ghasemi A, Katebi B, Nemat-Gorgani M. Role of surface oxygen-containing functional groups of graphene oxide quantum dots on amyloid fibrillation of two model proteins. PLoS One 2020; 15:e0244296. [PMID: 33362209 PMCID: PMC7757872 DOI: 10.1371/journal.pone.0244296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
There are many reports demonstrating that various derivatives of carbon nanoparticles are effective inhibitors of protein aggregation. As surface structural features of nanoparticles play a key role on modulating amyloid fibrillation process, in the present in vitro study, bovine insulin and hen egg white lysozyme (HEWL) were selected as two model proteins to investigate the reducing effect of graphene oxide quantum dots (GOQDs) on their assembly under amyloidogenic conditions. GOQDs were prepared through direct pyrolysis of citric acid, and the reduction step was carried out using ascorbic acid. The prepared nanoparticles were characterized by UV-Vis, X-ray photoelectron, and FT-IR spectroscopies, transmission electron and atomic force microscopies, zeta potential measurement, and Nile red fluorescence assay. They showed the tendencies to modulate the assembly of the proteins through different mechanisms. While GOQDs appeared to have the capacity to inhibit fibrillation, the presence of reduced GOQDs (rGOQDs) was found to promote protein assembly via shortening the nucleation phase, as suggested by ThT fluorescence data. Moreover, the structures produced in the presence of GOQDs or rGOQDs were totally nontoxic. We suggest that surface properties of these particles may be part of the differences in their mechanism(s) of action.
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Affiliation(s)
| | - Mohsen Mahdavimehr
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
- * E-mail: ,
| | - Nasser Nikfarjam
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bentolhoda Katebi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Mohsen Nemat-Gorgani
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States of America
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15
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Sha J, Chen X, Ma L. Concentration‐dependent conformation transition of regenerated silk fibroin induced by graphene oxide nanosheets incorporation. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/polb.24895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jin Sha
- School of Mechanical and Power Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Xin Chen
- School of Mechanical and Power Engineering, East China University of Science and Technology Shanghai 200237 China
| | - Liang Ma
- School of Mechanical and Power Engineering, East China University of Science and Technology Shanghai 200237 China
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16
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Protein-surface interactions at the nanoscale: Atomistic simulations with implicit solvent models. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Mohajeri M, Behnam B, Barreto GE, Sahebkar A. Carbon nanomaterials and amyloid-beta interactions: potentials for the detection and treatment of Alzheimer's disease? Pharmacol Res 2019; 143:186-203. [DOI: 10.1016/j.phrs.2019.03.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 01/24/2023]
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18
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Ortega M, Vilhena JG, Rubio-Pereda P, Serena PA, Pérez R. Assessing the Accuracy of Different Solvation Models To Describe Protein Adsorption. J Chem Theory Comput 2019; 15:2548-2560. [PMID: 30822382 DOI: 10.1021/acs.jctc.8b01060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In protein adsorption, the surrounding solvent has an important role in mediating protein-surface interactions. Therefore, it is of paramount importance that the solvent methods employed to model these kinds of processes are able to correctly capture the complex mechanisms occurring in the protein-water-surface interface. Here, we test the suitability of the two most popular implicit solvent methods based on the Generalized Born formalism to describe the adsorption process of the immunoglobulin G (IgG) on a hydrophobic graphene surface. Our results show that in both cases, IgG experiences an extreme and early (in less than 40 ns) unfolding as a result of the adsorption to the surface in contrast with previous experimental findings. A detailed energy decomposition analysis of explicit and implicit solvent simulations reveals that this discrepancy arises from the ill-characterization of two energy components in implicit solvent methods. These findings help to elucidate how implicit solvent models may be improved to accurately characterize the protein adsorption process.
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Affiliation(s)
| | - J G Vilhena
- Department of Physics , University of Basel , Klingelbergstrasse 82 , CH-4056 Basel , Switzerland
| | - Pamela Rubio-Pereda
- Instituto de Ciencia de Materiales de Madrid (ICMM) , CSIC , c/Sor Juana Ines de la Cruz 3 , E-28049 Madrid , Spain.,Centro de Investigación Científica y de Educación Superior de Ensenada 3918 , 22860 Ensenada , Baja California , Mexico
| | - P A Serena
- Instituto de Ciencia de Materiales de Madrid (ICMM) , CSIC , c/Sor Juana Ines de la Cruz 3 , E-28049 Madrid , Spain
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19
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Ebrahim-Habibi MB, Ghobeh M, Mahyari FA, Rafii-Tabar H, Sasanpour P. An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study. Sci Rep 2019; 9:1273. [PMID: 30718580 PMCID: PMC6362288 DOI: 10.1038/s41598-018-37311-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.
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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.
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20
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Yu L, Yang Y, Wang C. Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:35-60. [PMID: 31713196 DOI: 10.1007/978-981-13-9791-2_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter intends to review the progress in obtaining site-specific structural information for peptide assemblies using scanning tunneling microscopy. The effects on assembly propensity due to mutations and modifications in peptide sequences, small organic molecules and conformational transitions of peptides are identified. The obtained structural insights into the sequence-dependent assembly propensity could inspire rational design of peptide architectures at the molecular level.
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Affiliation(s)
- Lanlan Yu
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China
| | - Yanlian Yang
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China
| | - Chen Wang
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China.
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21
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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: 6.7] [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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22
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Kim T, Cho M, Yu KJ. Flexible and Stretchable Bio-Integrated Electronics Based on Carbon Nanotube and Graphene. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1163. [PMID: 29986539 PMCID: PMC6073353 DOI: 10.3390/ma11071163] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 11/23/2022]
Abstract
Scientific and engineering progress associated with increased interest in healthcare monitoring, therapy, and human-machine interfaces has rapidly accelerated the development of bio-integrated multifunctional devices. Recently, compensation for the cons of existing materials on electronics for health care systems has been provided by carbon-based nanomaterials. Due to their excellent mechanical and electrical properties, these materials provide benefits such as improved flexibility and stretchability for conformal integration with the soft, curvilinear surfaces of human tissues or organs, while maintaining their own unique functions. This review summarizes the most recent advanced biomedical devices and technologies based on two most popular carbon based materials, carbon nanotubes (CNTs) and graphene. In the beginning, we discuss the biocompatibility of CNTs and graphene by examining their cytotoxicity and/or detrimental effects on the human body for application to bioelectronics. Then, we scrutinize the various types of flexible and/or stretchable substrates that are integrated with CNTs and graphene for the construction of high-quality active electrode arrays and sensors. The convergence of these carbon-based materials and bioelectronics ensures scalability and cooperativity in various fields. Finally, future works with challenges are presented in bio-integrated electronic applications with these carbon-based materials.
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Affiliation(s)
- Taemin Kim
- School of Electrical Engineering, Yonsei University, Seoul 03722, Korea.
| | - Myeongki Cho
- School of Electrical Engineering, Yonsei University, Seoul 03722, Korea.
| | - Ki Jun Yu
- School of Electrical Engineering, Yonsei University, Seoul 03722, Korea.
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23
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Yu ZS, Gao YY, Wang XG, Zhou GQ, Zeng SW, Chen JL. Comparison of Adsorption of Proteins at Different Sizes on Pristine Graphene and Graphene Oxide. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1707138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Zuo-si Yu
- School of Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Yi-yi Gao
- School of Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Xiao-gang Wang
- School of Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Guo-quan Zhou
- School of Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Song-wei Zeng
- School of Information and Industry, Zhejiang A & F University, Hangzhou 311300, China
| | - Jun-lang Chen
- School of Sciences, Zhejiang A & F University, Hangzhou 311300, China
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24
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Verma A, Parashar A, Packirisamy M. Atomistic modeling of graphene/hexagonal boron nitride polymer nanocomposites: a review. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1346] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Akarsh Verma
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee India
| | - Avinash Parashar
- Department of Mechanical and Industrial Engineering Indian Institute of Technology Roorkee India
| | - M. Packirisamy
- Department of Mechanical and Industrial Engineering Concordia University Montreal Canada
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25
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Walsh TR, Knecht MR. Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials. Chem Rev 2017; 117:12641-12704. [DOI: 10.1021/acs.chemrev.7b00139] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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26
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Wang L, Zhang Y, Wu A, Wei G. Designed graphene-peptide nanocomposites for biosensor applications: A review. Anal Chim Acta 2017; 985:24-40. [PMID: 28864192 DOI: 10.1016/j.aca.2017.06.054] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/20/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
Abstract
The modification of graphene with biomacromolecules like DNA, protein, peptide, and others extends the potential applications of graphene materials in various fields. The bound biomacromolecules could improve the biocompatibility and bio-recognition ability of graphene-based nanocomposites, therefore could greatly enhance their biosensing performances on both selectivity and sensitivity. In this review, we presented a comprehensive introduction and discussion on recent advance in the synthesis and biosensor applications of graphene-peptide nanocomposites. The biofunctionalization of graphene with specifically designed peptides, and the synthesis strategies of graphene-peptide (monomer, nanofibrils, and nanotubes) nanocomposites were demonstrated. On the other hand, the fabrication of graphene-peptide nanocomposite based biosensor architectures for electrochemical, fluorescent, electronic, and spectroscopic biosensing were further presented. This review includes nearly all the studies on the fabrication and applications of graphene-peptide based biosensors recently, which will promote the future developments of graphene-based biosensors in biomedical detection and environmental analysis.
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Affiliation(s)
- Li Wang
- Key Laboratory of Preparation and Application of Environmental Friendly Materials (Jilin Normal University), Ministry of Education, Changchun, 130103, PR China.
| | - Yujie Zhang
- CAS Key Laboratory of Magnetic Materials and Devices, Key Laboratory of Additive Manufacturing Materials of Zhejiang Province, Division of Functional Materials and Nanodevices, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang, 315201, PR China
| | - Aiguo Wu
- CAS Key Laboratory of Magnetic Materials and Devices, Key Laboratory of Additive Manufacturing Materials of Zhejiang Province, Division of Functional Materials and Nanodevices, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang, 315201, PR China
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, Bremen, D-28359, Germany.
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27
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Rubio-Pereda P, Vilhena JG, Takeuchi N, Serena PA, Pérez R. Albumin (BSA) adsorption onto graphite stepped surfaces. J Chem Phys 2017; 146:214704. [PMID: 28595417 PMCID: PMC5457296 DOI: 10.1063/1.4984037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 05/10/2017] [Indexed: 11/14/2022] Open
Abstract
Nanomaterials are good candidates for the design of novel components with biomedical applications. For example, nano-patterned substrates may be used to immobilize protein molecules in order to integrate them in biosensing units. Here, we perform long MD simulations (up to 200 ns) using an explicit solvent and physiological ion concentrations to characterize the adsorption of bovine serum albumin (BSA) onto a nano-patterned graphite substrate. We have studied the effect of the orientation and step size on the protein adsorption and final conformation. Our results show that the protein is stable, with small changes in the protein secondary structure that are confined to the contact area and reveal the influence of nano-structuring on the spontaneous adsorption, protein-surface binding energies, and protein mobility. Although van der Waals (vdW) interactions play a dominant role, our simulations reveal the important role played by the hydrophobic lipid-binding sites of the BSA molecule in the adsorption process. The complex structure of these sites, that incorporate residues with different hydrophobic character, and their flexibility are crucial to understand the influence of the ion concentration and protein orientation in the different steps of the adsorption process. Our study provides useful information for the molecular engineering of components that require the immobilization of biomolecules and the preservation of their biological activity.
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Affiliation(s)
- Pamela Rubio-Pereda
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/ Sor Juana Inés de la Cruz 3, E-28049 Madrid, Spain
| | - J G Vilhena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/ Sor Juana Inés de la Cruz 3, E-28049 Madrid, Spain
| | - Noboru Takeuchi
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, 22800 Ensenada, Baja California, Mexico
| | - Pedro A Serena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/ Sor Juana Inés de la Cruz 3, E-28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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28
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Li J, Yang Y, Mao Z, Huang W, Qiu T, Wu Q. Enhanced Resolution of DNA Separation Using Agarose Gel Electrophoresis Doped with Graphene Oxide. NANOSCALE RESEARCH LETTERS 2016; 11:404. [PMID: 27637896 PMCID: PMC5025413 DOI: 10.1186/s11671-016-1609-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/02/2016] [Indexed: 05/23/2023]
Abstract
In this work, a novel agarose gel electrophoresis strategy has been developed for separation of DNA fragments by doping graphene oxide (GO) into agarose gel. The results show that the addition of GO into agarose gel significantly improved the separation resolution of DNA fragments by increasing the shift distances of both the single DNA fragments and the adjacent DNA fragments and completely eliminating the background noise derived from the diffusion of the excessive ethidium bromide (EB) dye in the gel after electrophoresis. The improved resolution of DNA fragments in GO-doped agarose gel could be attributed to the successive adsorption-desorption processes between DNA fragments and GO sheets, while the elimination of the background noise could be attributed to the adsorption of the excessive EB dye on the surface of GO sheets and high fluorescence quenching efficiency of GO. These results provide promising potential for graphene and its derivate utilized in various electrophoresis techniques for separation and detection of DAN fragments and other biomolecules.
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Affiliation(s)
- Jialiang Li
- School of Chemical Engineering, Shandong University of Technology, Zibo, 255049 China
| | - Yushi Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Material and Engineering Center, Wuhan University of Technology, Wuhan, 430070 China
| | - Zhou Mao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Material and Engineering Center, Wuhan University of Technology, Wuhan, 430070 China
| | - Wenjie Huang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Material and Engineering Center, Wuhan University of Technology, Wuhan, 430070 China
| | - Tong Qiu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Material and Engineering Center, Wuhan University of Technology, Wuhan, 430070 China
| | - Qingzhi Wu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Material and Engineering Center, Wuhan University of Technology, Wuhan, 430070 China
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29
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Abstract
Recognition and manipulation of graphene edges enable the control of physical properties of graphene-based devices. Recently, the authors have identified a peptide that preferentially binds to graphene edges from a combinatorial peptide library. In this study, the authors examine the functional basis for the edge binding peptide using experimental and computational methods. The effect of amino acid substitution, sequence context, and solution pH value on the binding of the peptide to graphene has been investigated. The N-terminus glutamic acid residue plays a key role in recognizing and binding to graphene edges. The protonation, substitution, and positional context of the glutamic acid residue impact graphene edge-binding. Our findings provide insights into the binding mechanisms and the design of peptides for recognizing and functionalizing graphene edges.
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30
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Liang L, Kong Z, Kang Z, Wang H, Zhang L, Shen JW. Theoretical Evaluation on Potential Cytotoxicity of Graphene Quantum Dots. ACS Biomater Sci Eng 2016; 2:1983-1991. [PMID: 33440534 DOI: 10.1021/acsbiomaterials.6b00390] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Owing to unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the field of electrochemical biosensors, bioimaging, drug delivery, et cetera. Its biosafety and potential cytotoxicity to human and animal cells has been a growing concern in recent years. In this work, the potential cytotoxicity of GQDs was evaluated by molecular dynamics simulations. Our simulation demonstrates that small size GQDs could easily permeate into the lipid membrane in a vertical way. It is relatively difficult to permeate into the lipid membrane for GQDs that are larger than GQD61 on the nanosecond time-scale. The thickness of the POPC membrane could even be affected by the small size of GQDs. Free energy calculations revealed that the free energy barrier of GQD permeation through the lipid membrane could greatly change with the change of GQD size. Under high GQD concentration, the GQD molecules could rapidly aggregate in water but disaggregate after entering into the membrane interior. Moreover, high concentrations of GQDs could induce changes in the structure properties and diffusion properties of the lipid bilayer, and it may affect the cell signal transduction. However, GQDs with relatively small size are not large enough to mechanically damage the lipid membrane. Our results suggest that the cytotoxicity of GQDs with small size is low and may be appropriate for biomedical application.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, No. 1, Second Street, Jianggan District, Hangzhou, 310018, People's Republic of China
| | - Zhe Kong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, No. 1, Second Street, Jianggan District, Hangzhou, 310018, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry, Zhejiang University, Zheda Road 38, Hangzhou, 310028, People's Republic of China.,Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hongbo Wang
- College of Automation, Hangzhou Dianzi University, No. 1, Second Street, Jianggan District, Hangzhou 310018, People's Republic of China
| | - Li Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, No. 2, Second Street, Jianggan District, Hangzhou, 310012, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Xuelin Street 16, Jianggan District, Hangzhou 310016, People's Republic of China
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31
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Vilhena JG, Dumitru AC, Herruzo ET, Mendieta-Moreno JI, Garcia R, Serena PA, Pérez R. Adsorption orientations and immunological recognition of antibodies on graphene. NANOSCALE 2016; 8:13463-13475. [PMID: 27352029 DOI: 10.1039/c5nr07612a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors.
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Affiliation(s)
- J G Vilhena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain. and Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - A C Dumitru
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain.
| | - Elena T Herruzo
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain.
| | - Jesús I Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and Centro de Biología Molecular Severo Ochoa, CSIC-UAM, E-28049 Madrid, Spain
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain.
| | - P A Serena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and IFIMAC - Condensed Matter Physics Center, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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32
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Zeng S, Zhou G, Guo J, Zhou F, Chen J. Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide. Sci Rep 2016; 6:24906. [PMID: 27097898 PMCID: PMC4838942 DOI: 10.1038/srep24906] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/05/2016] [Indexed: 11/09/2022] Open
Abstract
Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO.
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Affiliation(s)
- Songwei Zeng
- School of Information and Industry, Zhejiang A & F University, Lin’an 311300, China
| | - Guoquan Zhou
- Key Laboratory of Chemical Utilization of Forestry Biomass of Zhejiang Province, School of Sciences, Zhejiang A & F University, Lin’an 311300, China
| | - Jianzhong Guo
- Key Laboratory of Chemical Utilization of Forestry Biomass of Zhejiang Province, School of Sciences, Zhejiang A & F University, Lin’an 311300, China
| | - Feng Zhou
- Zhe Jiang province environmental radiation monitoring center, Hangzhou 310012, China
| | - Junlang Chen
- School of Information and Industry, Zhejiang A & F University, Lin’an 311300, China
- Key Laboratory of Chemical Utilization of Forestry Biomass of Zhejiang Province, School of Sciences, Zhejiang A & F University, Lin’an 311300, China
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33
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Graphene Functionalized Scaffolds Reduce the Inflammatory Response and Supports Endogenous Neuroblast Migration when Implanted in the Adult Brain. PLoS One 2016; 11:e0151589. [PMID: 26978268 PMCID: PMC4792446 DOI: 10.1371/journal.pone.0151589] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/01/2016] [Indexed: 01/02/2023] Open
Abstract
Electroactive materials have been investigated as next-generation neuronal tissue engineering scaffolds to enhance neuronal regeneration and functional recovery after brain injury. Graphene, an emerging neuronal scaffold material with charge transfer properties, has shown promising results for neuronal cell survival and differentiation in vitro. In this in vivo work, electrospun microfiber scaffolds coated with self-assembled colloidal graphene, were implanted into the striatum or into the subventricular zone of adult rats. Microglia and astrocyte activation levels were suppressed with graphene functionalization. In addition, self-assembled graphene implants prevented glial scarring in the brain 7 weeks following implantation. Astrocyte guidance within the scaffold and redirection of neuroblasts from the subventricular zone along the implants was also demonstrated. These findings provide new functional evidence for the potential use of graphene scaffolds as a therapeutic platform to support central nervous system regeneration.
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34
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Vilhena JG, Rubio-Pereda P, Vellosillo P, Serena PA, Pérez R. Albumin (BSA) Adsorption over Graphene in Aqueous Environment: Influence of Orientation, Adsorption Protocol, and Solvent Treatment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1742-1755. [PMID: 26799950 DOI: 10.1021/acs.langmuir.5b03170] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report 150 ns explicit solvent MD simulations of the adsorption on graphene of albumin (BSA) in two orientations and using two different adsorption protocols, i.e., free and forced adsorption. Our results show that free adsorption occurs with little structural rearrangements. Even taking adsorption to an extreme, by forcing it with a 5 nN downward force applied during the initial 20 ns, we show that along a particular orientation BSA is able to preserve the structural properties of the majority of its binding sites. Furthermore, in all the cases considered in this work, the ibuprofen binding site has shown a strong resilience to structural changes. Finally, we compare these results with implicit solvent simulations and find that the latter predicts an extreme protein unfolding upon adsorption. The origin of this discrepancy is attributed to a poor description of the water entropic forces at interfaces in the implicit solvent methods.
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Affiliation(s)
- J G Vilhena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain
| | - Pamela Rubio-Pereda
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain
- Centro de Investigación Científica y de Educación Superior de Ensenada 3918, Postal Code 22860, Ensenada, Baja California, Mexico
| | - Perceval Vellosillo
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain
| | - P A Serena
- Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, c/Sor Juana Ines de la Cruz 3, E-28049 Madrid, Spain
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35
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Ghadari R. A study on the interactions of amino acids with nitrogen doped graphene; docking, MD simulation, and QM/MM studies. Phys Chem Chem Phys 2016; 18:4352-61. [DOI: 10.1039/c5cp06734k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding properties of twenty amino acids with nitrogen-doped graphene structures were studied using docking, MD simulation, and QM/MM methods.
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Affiliation(s)
- Rahim Ghadari
- Computational Chemistry Laboratory
- Department of Organic and Biochemistry
- Faculty of Chemistry
- University of Tabriz
- 51664 Tabriz
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36
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Park S, Kang YJ, Majd S. A Review of Patterned Organic Bioelectronic Materials and their Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:7583-7619. [PMID: 26397962 DOI: 10.1002/adma.201501809] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/17/2015] [Indexed: 06/05/2023]
Abstract
Organic electronic materials are rapidly emerging as superior replacements for a number of conventional electronic materials, such as metals and semiconductors. Conducting polymers, carbon nanotubes, graphenes, organic light-emitting diodes, and diamond films fabricated via chemical vapor deposition are the most popular organic bioelectronic materials that are currently under active research and development. Besides the capability to translate biological signals to electrical signals or vice versa, organic bioelectronic materials entail greater biocompatibility and biodegradability compared to conventional electronic materials, which makes them more suitable for biomedical applications. When patterned, these materials bring about numerous capabilities to perform various tasks in a more-sophisticated and high-throughput manner. Here, we provide an overview of the unique properties of organic bioelectronic materials, different strategies applied to pattern these materials, and finally their applications in the field of biomedical engineering, particularly biosensing, cell and tissue engineering, actuators, and drug delivery.
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Affiliation(s)
- SooHyun Park
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - You Jung Kang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sheereen Majd
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA, 16802, USA
- Materials Research Institute, The Pennsylvania State University, University Park, PA, 16802, USA
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37
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Cheng Y, Koh LD, Li D, Ji B, Zhang Y, Yeo J, Guan G, Han MY, Zhang YW. Peptide-Graphene Interactions Enhance the Mechanical Properties of Silk Fibroin. ACS APPLIED MATERIALS & INTERFACES 2015; 7:21787-96. [PMID: 26364925 DOI: 10.1021/acsami.5b05615] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Studies reveal that biomolecules can form intriguing molecular structures with fascinating functionalities upon interaction with graphene. Then, interesting questions arise. How does silk fibroin interact with graphene? Does such interaction lead to an enhancement in its mechanical properties? In this study, using large-scale molecular dynamics simulations, we first examine the interaction of graphene with several typical peptide structures of silk fibroin extracted from different domains of silk fibroin, including pure amorphous (P1), pure crystalline (P2), a segment from N-terminal (P3), and a combined amorphous and crystalline segment (P4), aiming to reveal their structural modifications. Our study shows that graphene can have intriguing influences on the structures formed by the peptides with sequences representing different domains of silk fibroin. In general, for protein domains with stable structure and strong intramolecular interaction (e.g., β-sheets), graphene tends to compete with the intramolecular interactions and thus weaken the interchain interaction and reduce the contents of β-sheets. For the silk domains with random or less ordered secondary structures and weak intramolecular interactions, graphene tends to enhance the stability of peptide structures; in particular, it increases the contents of helical structures. Thereafter, tensile simulations were further performed on the representative peptides to investigate how such structure modifications affect their mechanical properties. It was found that the strength and resilience of the peptides are enhanced through their interaction with graphene. The present work reveals interesting insights into the interactions between silk peptides and graphene, and contributes in the efforts to enhance the mechanical properties of silk fibroin.
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Affiliation(s)
- Yuan Cheng
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
| | - Leng-Duei Koh
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
- Department of Biomedical Engineering, National University of Singapore , Singapore 117575, Singapore
| | - Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology , Beijing 100081, China
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology , Beijing 100081, China
| | - Yingyan Zhang
- School of Computing, Engineering, and Mathematics, Western Sydney University , Locked Bag 1797, Penrith NSW 2751, Australia
| | - Jingjie Yeo
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
| | - Guijian Guan
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
| | - Ming-Yong Han
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
- Department of Biomedical Engineering, National University of Singapore , Singapore 117575, Singapore
| | - Yong-Wei Zhang
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
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38
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Wang X, Weber JK, Liu L, Dong M, Zhou R, Li J. A novel form of β-strand assembly observed in Aβ(33-42) adsorbed onto graphene. NANOSCALE 2015; 7:15341-15348. [PMID: 26331805 DOI: 10.1039/c5nr00555h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.
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Affiliation(s)
- Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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39
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Penna MJ, Mijajlovic M, Tamerler C, Biggs MJ. Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface. SOFT MATTER 2015; 11:5192-203. [PMID: 25920450 DOI: 10.1039/c5sm00123d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).
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Affiliation(s)
- M J Penna
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
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40
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Kong L, Enders A, Rahman TS, Dowben PA. Molecular adsorption on graphene. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:443001. [PMID: 25287516 DOI: 10.1088/0953-8984/26/44/443001] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H(2)O, H(2), O(2), CO, NO(2), NO, and NH(3)), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH(2), An-CH(3), An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene's electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.
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Affiliation(s)
- Lingmei Kong
- Department of Physics and Astronomy, Nebraska Center for Materials and Nanoscience, Theodore Jorgensen Hall, 855 North 16th Street, University of Nebraska, PO Box 880299, Lincoln, NE 68588-0299, USA
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41
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Xie L, Luo Y, Lin D, Xi W, Yang X, Wei G. The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment. NANOSCALE 2014; 6:9752-62. [PMID: 25004796 DOI: 10.1039/c4nr01005a] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Amyloid deposits are implicated in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. Increasing data show that nanoparticles can retard or promote the fibrillation of amyloid-β (Aβ) peptides depending on the physicochemical properties of nanoparticles, however, the underlying molecular mechanism remains elusive. In this study, our replica exchange molecular dynamics (REMD) simulations show that fullerene nanoparticle - C60 (with a fullerene : peptide molar ratio greater than 1 : 8) can dramatically prevent β-sheet formation of Aβ(16-22) peptides. Atomic force microscopy (AFM) experiments further confirm the inhibitory effect of C60 on Aβ(16-22) fibrillation, in support of our REMD simulations. An important finding from our REMD simulations is that fullerene C180, albeit with the same number of carbon atoms as three C60 molecules (3C60) and smaller surface area than 3C60, displays an unexpected stronger inhibitory effect on the β-sheet formation of Aβ(16-22) peptides. A detailed analysis of the fullerene-peptide interaction reveals that the stronger inhibition of β-sheet formation by C180 results from the strong hydrophobic and aromatic-stacking interactions of the fullerene hexagonal rings with the Phe rings relative to the pentagonal rings. The strong interactions between the fullerene nanoparticles and Aβ(16-22) peptides significantly weaken the peptide-peptide interaction that is important for β-sheet formation, thus retarding Aβ(16-22) fibrillation. Overall, our studies reveal the significant role of fullerene hexagonal rings in the inhibition of Aβ(16-22) fibrillation and provide novel insight into the development of drug candidates against Alzheimer's disease.
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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, 220 Handan Road, Shanghai, 200433, China.
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42
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Zhou R, Gao H. Cytotoxicity of graphene: recent advances and future perspective. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:452-74. [PMID: 24957946 DOI: 10.1002/wnan.1277] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 01/22/2023]
Abstract
Graphene, a unique two-dimensional single-atom-thin nanomaterial with exceptional structural, mechanical, and electronic properties, has spurred an enormous interest in many fields, including biomedical applications, which at the same time ignites a growing concern on its biosafety and potential cytotoxicity to human and animal cells. In this review, we present a summary of some very recent studies on this important subject with both experimental and theoretical approaches. The molecular interactions of graphene with proteins, DNAs, and cell membranes (both bacteria and mammalian cells) are discussed in detail. Severe distortions in structures and functions of these biomacromolecules by graphene are identified and characterized. For example, the graphene is shown to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules directly. More interestingly, this cytotoxicity has been shown to have implications in de novo design of nanomedicine, such as graphene-based band-aid, a potential 'green' antibiotics due to its strong physical-based (instead of chemical-based) antibacterial capability. These studies have provided a better understanding of graphene nanotoxicity at both cellular and molecular levels, and also suggested therapeutic potential by using graphene's cytotoxicity against bacteria cells.
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Affiliation(s)
- Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA; Department of Chemistry, Columbia University, New York, NY, USA
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43
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Jimenez-Cruz CA, Kang SG, Zhou R. Large scale molecular simulations of nanotoxicity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:329-43. [PMID: 24894909 DOI: 10.1002/wsbm.1271] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/02/2014] [Accepted: 05/19/2014] [Indexed: 12/25/2022]
Abstract
The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells.
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Affiliation(s)
- Camilo A Jimenez-Cruz
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA
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44
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Deng X, Tang H, Jiang J. Recent progress in graphene-material-based optical sensors. Anal Bioanal Chem 2014; 406:6903-16. [DOI: 10.1007/s00216-014-7895-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 12/11/2022]
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45
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Rathinam NK, Saravanan C, Parimal P, Perumal V, Perumal M. Molecular interactions of graphene with HIV-Vpr, Nef and Gag proteins: A new approach for treating HIV infections. KOREAN J CHEM ENG 2014. [DOI: 10.1007/s11814-014-0049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Long F, Zhu A, Shi H, Wang H. Hapten-Grafted Graphene as a Transducer for Homogeneous Competitive Immunoassay of Small Molecules. Anal Chem 2014; 86:2862-6. [DOI: 10.1021/ac500347n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Feng Long
- School of Environment
and Natural Resources, Renmin University of China, Haidian, Beijing 100872, China
| | - Anna Zhu
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Hanchang Shi
- State Key Joint
Laboratory of ESPC, School of Evironment, Tsinghua University, Beijing 100084, China
| | - Hongchen Wang
- School of Environment
and Natural Resources, Renmin University of China, Haidian, Beijing 100872, China
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47
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Guo J, Yao X, Ning L, Wang Q, Liu H. The adsorption mechanism and induced conformational changes of three typical proteins with different secondary structural features on graphene. RSC Adv 2014. [DOI: 10.1039/c3ra45876h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Yang Y, Wang C. Single-molecule studies on individual peptides and peptide assemblies on surfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120311. [PMID: 24000363 DOI: 10.1098/rsta.2012.0311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This review is intended to reflect the recent progress in single-molecule studies of individual peptides and peptide assemblies on surfaces. The structures and the mechanism of peptide assembly are discussed in detail. The contents include the following topics: structural analysis of single peptide molecules, adsorption and assembly of peptides on surfaces, folding structures of the amyloid peptides, interaction between amyloid peptides and dye or drug molecules, and modulation of peptide assemblies by small molecules. The explorations of peptide adsorption and assembly will benefit the understanding of the mechanisms for protein-protein interactions, protein-drug interactions and the pathogenesis of amyloidoses. The investigations on peptide assembly and its modulations could also provide a potential approach towards the treatment of the amyloidoses.
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Affiliation(s)
- Yanlian Yang
- National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
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Zhang M, Mao X, Yu Y, Wang CX, Yang YL, Wang C. Nanomaterials for reducing amyloid cytotoxicity. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:3780-801. [PMID: 23722464 DOI: 10.1002/adma.201301210] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 05/20/2023]
Abstract
This review is intended to reflect the recent progress on therapeutic applications of nanomaterials in amyloid diseases. The progress on anti-amyloid functions of various nanomaterials including inorganic nanoparticles, polymeric nanoparticles, carbon nanomaterials and biomolecular aggregates, is reviewed and discussed. The main functionalization strategies for general nanoparticle modifications are reviewed for potential applications of targeted therapeutics. The interaction mechanisms between amyloid peptides and nanomaterials are discussed from the perspectives of dominant interactions and kinetics. The encapsulation of anti-amyloid drugs, targeted drug delivery, controlled drug release and drug delivery crossing blood brain barrier by application of nanomaterials would also improve the therapeutics of amyloid diseases.
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Affiliation(s)
- Min Zhang
- National Center for Nanoscience and Technology, Beijing 100190, China
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Li C, Mezzenga R. The interplay between carbon nanomaterials and amyloid fibrils in bio-nanotechnology. NANOSCALE 2013; 5:6207-6218. [PMID: 23744243 DOI: 10.1039/c3nr01644g] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent advances in bio-nanotechnology have not only rapidly broadened the applications and scope of hybrid nanomaterials in biological fields, but also greatly enriched the examples of ordered materials based on supramolecular self-assembly. Among eminent examples of functional nanostructured materials of undisputed impact in nanotechnology and biological environments, carbon nanomaterials (such as fullerenes, carbon nanotubes and graphene) and amyloid fibrils have attracted great attention because of their unique architectures and exceptional physical properties. Nonetheless, combination of these two classes of nanomaterials into functional hybrids is far from trivial. For example, the presence of carbon nanomaterials can offer either an inhibitory effect or promotion of amyloid fibrillation, depending on the structural architectures of carbon nanomaterials and the starting amyloid proteins/peptides considered. To date, numerous studies have been devoted to evaluating both the biological toxicity of carbon nanomaterials and their use in developing therapies for amyloidosis. At the same time, hybridization of these two classes of nanomaterials offers new possibilities for combining some of their desirable properties into nanocomposites of possible use in electronics, actuators, sensing, biomedicine and structural materials. This review describes recent developments in the hybridization of carbon nanomaterials and amyloid fibrils and discusses the current state of the art on the application of carbon nanomaterial-amyloid fibril hybrids in bio-nanotechnology.
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Affiliation(s)
- Chaoxu Li
- ETH Zurich, Food & Soft Materials, Department of Health Science & Technology, Zurich, Switzerland
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