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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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Qian Y, Di S, Wang L, Li Z. Recent advances in the synthesis and applications of graphene-polypeptide nanocomposites. J Mater Chem B 2021; 9:6521-6535. [PMID: 34318859 DOI: 10.1039/d1tb00779c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combination of peptides and graphene-derived materials provides a new way to prepare graphene-based nanocomposites with unique structures, properties, and functions. The modification of graphene with different polypeptides not only improves the biocompatibility and biological recognition ability of graphene-based materials, but also greatly expands their application fields. In this work, we summarize different interactions between graphene and polypeptides, and the synthesis methods of novel functional graphene-polypeptide nanocomposites based on the interactions in recent years (from 2016 to present). In addition, the potential applications of graphene-peptide hybrid nanocomposites in biomedicine, tissue engineering, biosensors, environmental science engineering, optoelectronic materials, and energy storage are introduced. We hope that this review will help readers to understand the methods and mechanisms of the modification of graphene surfaces with biomolecules, and promote readers to understand the synthesis and applications of graphene-based nanocomposites. This work may provide hints and references for the development of peptide sequence design, and biomedical and functional materials, and will help in designing and synthesizing novel graphene-based nanomaterials with unique properties and suitable for various applications in the future.
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Affiliation(s)
- Yuhong Qian
- College of Chemistry, Jilin Normal University, Siping 136000, P. R. China.
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3
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Label-free impedimetric miRNA-192 genosensor platform using graphene oxide decorated peptide nanotubes composite. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Narayan B, Herbert C, Rodriguez BJ, Brooks BR, Buchete NV. Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields. J Phys Chem B 2021; 125:5233-5242. [PMID: 33990140 PMCID: PMC8279545 DOI: 10.1021/acs.jpcb.1c01939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The self-assembling propensity of amyloid peptides such as diphenylalanine (FF) allows them to form ordered, nanoscale structures, with biocompatible properties important for biomedical applications. Moreover, piezoelectric properties allow FF molecules and their aggregates (e.g., FF nanotubes) to be aligned in a controlled way by the application of external electric fields. However, while the behavior of FF nanostructures emerges from the biophysical properties of the monomers, the detailed responses of individual peptides to both temperature and electric fields are not fully understood. Here, we study the temperature-dependent conformational dynamics of FF peptides solvated in explicit water molecules, an environment relevant to biomedical applications, by using an enhanced sampling method, replica exchange molecular dynamics (REMD), in conjunction with applied electric fields. Our simulations highlight and overcome possible artifacts that may occur during the setup of REMD simulations of explicitly solvated peptides in the presence of external electric fields, a problem particularly important in the case of short peptides such as FF. The presence of the external fields could overstabilize certain conformational states in one or more REMD replicas, leading to distortions of the underlying potential energy distributions observed at each temperature. This can be overcome by correcting the REMD initial conditions to include the lower-energy conformations induced by the external field. We show that the converged REMD data can be analyzed using a Markovian description of conformational states and show that a rather complex, 3-state, temperature-dependent conformational dynamics in the absence of electric fields collapses to only one of these states in the presence of the electric fields. These details on the temperature- and electric-field-dependent thermodynamic and kinetic properties of small FF amyloid peptides can be useful in understanding and devising new methods to control their aggregation-prone biophysical properties and, possibly, the structural and biophysical properties of FF molecular nanostructures.
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Affiliation(s)
- Brajesh Narayan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland
| | - Colm Herbert
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland
| | - Brian J Rodriguez
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Bernard R Brooks
- Laboratory of Computational Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nicolae-Viorel Buchete
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland
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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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Ariga K, Nishikawa M, Mori T, Takeya J, Shrestha LK, Hill JP. Self-assembly as a key player for materials nanoarchitectonics. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2019; 20:51-95. [PMID: 30787960 PMCID: PMC6374972 DOI: 10.1080/14686996.2018.1553108] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/23/2018] [Accepted: 11/25/2018] [Indexed: 05/07/2023]
Abstract
The development of science and technology of advanced materials using nanoscale units can be conducted by a novel concept involving combination of nanotechnology methodology with various research disciplines, especially supramolecular chemistry. The novel concept is called 'nanoarchitectonics' where self-assembly processes are crucial in many cases involving a wide range of component materials. This review of self-assembly processes re-examines recent progress in materials nanoarchitectonics. It is composed of three main sections: (1) the first short section describes typical examples of self-assembly research to outline the matters discussed in this review; (2) the second section summarizes self-assemblies at interfaces from general viewpoints; and (3) the final section is focused on self-assembly processes at interfaces. The examples presented demonstrate the strikingly wide range of possibilities and future potential of self-assembly processes and their important contribution to materials nanoarchitectonics. The research examples described in this review cover variously structured objects including molecular machines, molecular receptors, molecular pliers, molecular rotors, nanoparticles, nanosheets, nanotubes, nanowires, nanoflakes, nanocubes, nanodisks, nanoring, block copolymers, hyperbranched polymers, supramolecular polymers, supramolecular gels, liquid crystals, Langmuir monolayers, Langmuir-Blodgett films, self-assembled monolayers, thin films, layer-by-layer structures, breath figure motif structures, two-dimensional molecular patterns, fullerene crystals, metal-organic frameworks, coordination polymers, coordination capsules, porous carbon spheres, mesoporous materials, polynuclear catalysts, DNA origamis, transmembrane channels, peptide conjugates, and vesicles, as well as functional materials for sensing, surface-enhanced Raman spectroscopy, photovoltaics, charge transport, excitation energy transfer, light-harvesting, photocatalysts, field effect transistors, logic gates, organic semiconductors, thin-film-based devices, drug delivery, cell culture, supramolecular differentiation, molecular recognition, molecular tuning, and hand-operating (hand-operated) nanotechnology.
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Affiliation(s)
- Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | | | - Taizo Mori
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Jun Takeya
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Lok Kumar Shrestha
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
| | - Jonathan P. Hill
- WPI-MANA, National Institute for Materials Science (NIMS), Ibaraki, Japan
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Alattar N, Daud H, Al-Majmaie R, Zeulla D, Al-Rubeai M, Rice JH. Surface-enhanced Raman scattering for rapid hematopoietic stem cell differentiation analysis. APPLIED OPTICS 2018; 57:E184-E189. [PMID: 30117870 DOI: 10.1364/ao.57.00e184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/29/2018] [Indexed: 05/27/2023]
Abstract
Raman-spectroscopy-based methods, such as surface-enhanced Raman spectroscopy, are a well-evolved method to molecular fingerprint cell types. Here we demonstrate that surface-enhanced Raman spectroscopy can enable us to distinguish cell development stages of bone marrow hematopoietic stem cells towards red blood cells through the identification of specific surface-enhanced Raman spectroscopy biomarkers. The approach taken here is to allow cells to take in gold nanoparticles as Raman enhancement platforms for kinetic structural observations presented here through the view of the multidimensional parameter contribution, thereby enabling profiling of bone marrow hematopoietic stem cells acquired from proliferation (stage one), differentiation (stage two), and mature red blood cells (stage three).
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Liu D, Rahman MM, Ge C, Kim J, Lee JJ. Highly stable and conductive PEDOT:PSS/graphene nanocomposites for biosensor applications in aqueous medium. NEW J CHEM 2017. [DOI: 10.1039/c7nj03330c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A PEDOT:PSS/GNP electrode post-treated with H2SO4 stabilizes GNPs on an FTO substrate and improves the aqueous sensitivity and stability of dopamine detection.
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Affiliation(s)
- Dongtao Liu
- Department of Energy & Materials Engineering
- Dongguk University
- Seoul
- Korea
| | - Md. Mahbubur Rahman
- Nanotechnology Research Center and Department of Applied Life Science
- College of Biomedical and Health Science
- Konkuk University
- Chungju 380-701
- Korea
| | - Chuangye Ge
- Department of Energy & Materials Engineering
- Dongguk University
- Seoul
- Korea
| | - Jaecheon Kim
- Department of Energy & Materials Engineering
- Dongguk University
- Seoul
- Korea
| | - Jae-Joon Lee
- Department of Energy & Materials Engineering
- Dongguk University
- Seoul
- Korea
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