Biomolecular Interactions and Biological Responses of Emerging Two-Dimensional Materials and Aromatic Amino Acid Complexes

Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene

There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.

Insights into the interactions between cellulose and biological molecules

Understanding the interactions between carbohydrate polymer molecules and biomolecules is of primary significance for its application. In this paper, the interaction between cellulose and biomolecules was studied using density functional theory method, in which cellobiose, nucleobases, and aromatic amino acids were employed as the structural models of cellulose, DNA, and protein, respectively. Quantitative molecular surface electrostatic potential (ESP) results well represented how cellulose perceived by organism during the recognition. The structural and energetic studies of cellulose with biomolecules complexes show that weak interactions, such as hydrogen bonding interaction, vdW interaction, and pi-H interaction, play an important role in stabilizing these complexes. Through systematic wavefunction analysis, including reduced density gradient (RDG) and natural bond orbital (NBO) methods, the nature of these weak interactions was revealed and further graphically visualized. In-depth understanding of the interaction between cellobiose with biological model molecules may shed lights on the application of carbohydrate polymer-based materials in biological fields.

Design Strategies of Tumor-Targeted Delivery Systems Based on 2D Nanomaterials

Conventional chemotherapy and radiotherapy are nonselective and nonspecific for cell killing, causing serious side effects and threatening the lives of patients. It is of great significance to develop more accurate tumor-targeting therapeutic strategies. Nanotechnology is in a leading position to provide new treatment options for cancer, and it has great potential for selective targeted therapy and controlled drug release. 2D nanomaterials (2D NMs) have broad application prospects in the field of tumor-targeted delivery systems due to their special structure-based functions and excellent optical, electrical, and thermal properties. This review emphasizes the design strategies of tumor-targeted delivery systems based on 2D NMs from three aspects: passive targeting, active targeting, and tumor-microenvironment targeting, in order to promote the rational application of 2D NMs in clinical practice.

[Advances in separation and analysis of aromatic amino acids in food]

Amino acids are important building blocks of proteins in the human body, which are involved in many metabolic pathways. Patients with metabolic diseases such as phenylketonuria, tyrosinemia, and hepatic encephalopathy are genetically defective and cannot metabolize aromatic amino acids (AAA) in food; hence, a regular diet may lead to permanent physiological damage. For this reason, it is necessary to restrict the intake of AAA in their daily diet by limiting natural protein intake, while ensuring normal intake of low protein foods and supplementation with low-AAA protein equivalents. Sources of low-AAA protein equivalents currently rely on free amino acid complex mixtures and low-AAA peptides (also known as high-Fischer-ratio peptides), which have better absorption availability and palatability. AAA separation and analysis techniques are essential for the preparation and detection of low-AAA peptides. Researchers in this field have explored a variety of efficient adsorption materials to selectively remove AAA from complex protein hydrolysates and thus prepare low-AAA peptide foods, or to establish analysis strategies for AAA. Covering more than 70 publications on AAA removal and separation in the last decade from Web of Science Core Collection and China National Knowledge Infrastructure, this review analyzes the structural characteristics and physicochemical properties of AAA, and summarizes the technological progress of AAA removal based on adsorbents such as activated carbon and resin. The applications of two-dimensional nanomaterials, molecular imprinting, cyclodextrins, and metal-organic frameworks in AAA adsorption and analysis from three dimensions, i. e., sample pretreatment, chiral separation and adsorption sensing, are also reviewed. The mainstream adsorbents for AAA removal, such as activated carbon, still suffer from poor specificity and cause environmental pollution during post-use treatment. Existing AAA separating materials show impressive selective adsorption capability in food samples and chiral mixtures as well as high sensitivity in adsorption sensing. The development of an efficient detection technology for AAA may help in detecting trace AAA in food and in evaluating chiral AAA adulteration in food samples. By exploring the advantages and disadvantages of each type of technology, we provide support for the advancement of the removal and analysis techniques for AAA.

Biomimetic immunomodulation strategies for effective tissue repair and restoration

Inflammation plays a central role in wound healing following injury or disease and is mediated by a precise cascade of cellular and molecular events. Unresolved inflammatory processes lead to chronic inflammation and fibrosis, which can result in prolonged wound healing lasting months or years that hampers tissue function. Therapeutic interventions mediated by immunomodulatory drugs, cells, or biomaterials, are therefore most effective during the inflammatory phase of wound healing when a pro-regenerative environment is essential. In this review, we discuss the advantages of exploiting knowledge of the native tissue microenvironment to develop therapeutics capable of modulating the immune response and promoting functional tissue repair. In particular, we provide examples of the most recent biomimetic platforms proposed to accomplish this goal, with an emphasis on those able to induce macrophage polarization towards a pro-regenerative phenotype.

Graphene Oxide Nanosheets Interact and Interfere with SARS-CoV-2 Surface Proteins and Cell Receptors to Inhibit Infectivity

Nanotechnology can offer a number of options against coronavirus disease 2019 (COVID-19) acting both extracellularly and intracellularly to the host cells. Here, the aim is to explore graphene oxide (GO), the most studied 2D nanomaterial in biomedical applications, as a nanoscale platform for interaction with SARS-CoV-2. Molecular docking analyses of GO sheets on interaction with three different structures: SARS-CoV-2 viral spike (open state - 6VYB or closed state - 6VXX), ACE2 (1R42), and the ACE2-bound spike complex (6M0J) are performed. GO shows high affinity for the surface of all three structures (6M0J, 6VYB and 6VXX). When binding affinities and involved bonding types are compared, GO interacts more strongly with the spike or ACE2, compared to 6M0J. Infection experiments using infectious viral particles from four different clades as classified by Global Initiative on Sharing all Influenza Data (GISAID), are performed for validation purposes. Thin, biological-grade GO nanoscale (few hundred nanometers in lateral dimension) sheets are able to significantly reduce copies for three different viral clades. This data has demonstrated that GO sheets have the capacity to interact with SARS-CoV-2 surface components and disrupt infectivity even in the presence of any mutations on the viral spike. GO nanosheets are proposed to be further explored as a nanoscale platform for development of antiviral strategies against COVID-19.

Hybridization of Biomolecular Crystals and Low-Dimensional Materials

In cellular environments, metabolites, peptides, proteins, and other biomolecules can self-assemble into planar and fibrilar molecular crystals. We use atomistic molecular dynamics simulations to show that such biomolecular crystals coupled with low-dimensional materials can form stable hybrid superstructures. We discuss enantiopure and racemic TRP and PHE amino acid crystals adsorbed on or intercalated between graphene, phosphorene, and carbon nanotubes. While racemic biomolecular crystals tend to stay straight in solutions and when adsorbed on flat and cylindrical nanosurfaces, enantiopure crystals undergo twisting. Mixed material properties of these hybrid superstructures can be attractive in many applications.

Two-Dimensional Material-Based Biosensors for Virus Detection

Viral infections are one of the major causes of mortality and economic losses worldwide. Consequently, efficient virus detection methods are crucial to determine the infection prevalence. However, most detection methods face challenges related to false-negative or false-positive results, long response times, high costs, and/or the need for specialized equipment and staff. Such issues can be overcome by access to low-cost and fast response point-of-care detection systems, and two-dimensional materials (2DMs) can play a critical role in this regard. Indeed, the unique and tunable physicochemical properties of 2DMs provide many advantages for developing biosensors for viral infections with high sensitivity and selectivity. Fast, accurate, and reliable detection, even at early infection stages by the virus, can be potentially enabled by highly accessible surface interactions between the 2DMs and the analytes. High selectivity can be obtained by functionalization of the 2DMs with antibodies, nucleic acids, proteins, peptides, or aptamers, allowing for specific binding to a particular virus, viral fingerprints, or proteins released by the host organism. Multiplexed detection and discrimination between different virus strains are also feasible. In this Review, we present a comprehensive overview of the major advances of 2DM-based biosensors for the detection of viruses. We describe the main factors governing the efficient interactions between viruses and 2DMs, making them ideal candidates for the detection of viral infections. We also critically detail their advantages and drawbacks, providing insights for the development of future biosensors for virus detection. Lastly, we provide suggestions to stimulate research in the fast expanding field of 2DMs that could help in designing advanced systems for preventing virus-related pandemics.

Interfacial charge transfer with exfoliated graphene inhibits fibril formation in lysozyme amyloid

Amyloid fibrillation is known to contribute in a variety of diseases including neurodegenerative disorders (e.g., Alzheimer's and Parkinson's disease) and type II diabetes. The inhibition of fibrillation has been suggested as a possible therapeutic strategy to prevent neuronal and pancreatic β-cell death associated with amyloid diseases. To this end, strong hydrophobic and π-π interactions between proteins and nanomaterials at the nanobio interface could be used to mitigate the stacking of amyloid structures associated with fibrillation. In this study, the authors show that exfoliated graphene effectively inhibits the formation of amyloid fibrils using a model amyloid-forming protein, viz., hen egg white lysozyme (HEWL). While previous theoretical models posit that hydrophobic and π-π stacking interactions result in strong interactions between graphene and proteins, the authors experimentally identified the presence of additional interfacial charge transfer interactions between HEWL and graphene using micro-Raman spectroscopy and Kelvin probe force microscopy. Their photoluminescence spectroscopy and transmission electron microscopy studies evince that the interfacial charge transfer combined with hydrophobic and π-π stacking interactions, specifically between the nanomaterial and the amino acid tryptophan, increase HEWL adsorption on graphene and thereby inhibit amyloid fibrillation.

Graphene Oxide Nanosheets Tailored With Aromatic Dipeptide Nanoassemblies for a Tuneable Interaction With Cell Membranes

Engineered graphene-based derivatives are attractive and promising candidates for nanomedicine applications because of their versatility as 2D nanomaterials. However, the safe application of these materials needs to solve the still unanswered issue of graphene nanotoxicity. In this work, we investigated the self-assembly of dityrosine peptides driven by graphene oxide (GO) and/or copper ions in the comparison with the more hydrophobic diphenylalanine dipeptide. To scrutinize the peptide aggregation process, in the absence or presence of GO and/or Cu²⁺, we used atomic force microscopy, circular dichroism, UV-visible, fluorescence and electron paramagnetic resonance spectroscopies. The perturbative effect by the hybrid nanomaterials made of peptide-decorated GO nanosheets on model cell membranes of supported lipid bilayers was investigated. In particular, quartz crystal microbalance with dissipation monitoring and fluorescence recovery after photobleaching techniques were used to track the changes in the viscoelastic properties and fluidity of the cell membrane, respectively. Also, cellular experiments with two model tumour cell lines at a short time of incubation, evidenced the high potential of this approach to set up versatile nanoplatforms for nanomedicine and theranostic applications.

Adsorption of amino acids on graphene: assessment of current force fields

We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.

Graphene oxide touches blood: in vivo interactions of bio-coronated 2D materials

Graphene oxide is the hot topic in biomedical and pharmaceutical research of the current decade. However, its complex interactions with human blood components complicate the transition from the promising in vitro results to clinical settings. Even though graphene oxide is made with the same atoms as our organs, tissues and cells, its bi-dimensional nature causes unique interactions with blood proteins and biological membranes and can lead to severe effects like thrombogenicity and immune cell activation. In this review, we will describe the journey of graphene oxide after injection into the bloodstream, from the initial interactions with plasma proteins to the formation of the "biomolecular corona", and biodistribution. We will consider the link between the chemical properties of graphene oxide (and its functionalized/reduced derivatives), protein binding and in vivo response. We will also summarize data on biodistribution and toxicity in view of the current knowledge of the influence of the biomolecular corona on these processes. Our aim is to shed light on the unsolved problems regarding the graphene oxide corona to build the groundwork for the future development of drug delivery technology.

Graphene oxide down-regulates genes of the oxidative phosphorylation complexes in a glioblastoma

BACKGROUND

Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. We examined the effect of oxygenated, reduced and pristine graphene on the gene expression in glioblastoma U87 cell line.

RESULTS

Conducting microarrays and RT-qPCR analysis we explored that graphene oxide (rather than reduced graphene oxide and pristine graphene) down-regulates the mRNA expression of mitochondrial oxidative phosphorylation (OXPHOS) nuclear genes of complexes I, III, IV and V. The presented results provide first evidence for the hypothesis that the suppressed growth of GBM can be the consequence of down-regulation of OXPHOS protein expression and decreased ATP level.

CONCLUSIONS

We suggest that changes in the expression of OXPHOS genes identified in our study may mediate the anti-proliferative and anti-migratory effects of graphene oxide in glioblastoma cells. However, further investigations with different cell lines, regarding expression, regulation and activity of OXPHOS genes identified in our study is necessary to elucidate the mechanism mediating the anti-proliferative and anti-migratory effects of graphene oxide in glioblastoma cells.

Electronic transport in a graphene single layer: application in amino acid sensing

We modeled a type of field-effect transistor device based on graphene for the recognition of amino acids with a potential application in the building of a protein sequencer. The theoretical model used was a combination of density functional theory (DFT) with the non-equilibrium Green's function (NEGF) in order to describe the coherent transport in molecular devices. First, we studied the physisorption of each amino acid on a graphene sheet and we reported the adsorption energy, the adsorption distances, the equilibrium configuration and the charge transfer of ten amino acids that can be considered as representative of all of the amino acids: histidine (His), alanine (Ala), aspartic acid (Asp), tyrosine (Tyr), arginine (Arg), glutamic acid (Glu), glycine (Gly), phenylalanine (Phe), proline (Pro) and lysine (Lys). As a result, significant differences were found in the density of states (DOS) after adsorption and there was a change in the semi-metallic character of the graphene due to the lysine and arginine interactions. Furthermore, we noticed changes in the electrical characteristics of the devices, as the amino acids adsorbed onto the surface of the graphene. The curves of current vs. bias voltage (I-Vb) display a distinct response for each amino acid, i.e. the I-Vb curves produce a characteristic footprint for each amino acid. We identified a possible rectification mechanism related to the voltage profile asymmetry, where the amino acids can control the transport characteristics in the device, i.e. Lys and Phe amino acids physisorbed on graphene act as a molecular diode, where electrons can easily flow in one direction and decrease in the other. This may be promising for the prospect of biosensors: graphene could be used as an amino acid detector.

Assessing and Mitigating the Hazard Potential of Two-Dimensional Materials

The family of two-dimensional (2D) materials is comprised of a continually expanding palette of unique compositions and properties with potential applications in electronics, optoelectronics, energy capture and storage, catalysis, and nanomedicine. To accelerate the implementation of 2D materials in widely disseminated technologies, human health and environmental implications need to be addressed. While extensive research has focused on assessing the toxicity and environmental fate of graphene and related carbon nanomaterials, the potential hazards of other 2D materials have only recently begun to be explored. Herein, the toxicity and environmental fate of postcarbon 2D materials, such as transition metal dichalcogenides, hexagonal boron nitride, and black phosphorus, are reviewed as a function of their preparation methods and surface functionalization. Specifically, we delineate how the hazard potential of 2D materials is directly related to structural parameters and physicochemical properties and how experimental design is critical to the accurate elucidation of the underlying toxicological mechanisms. Finally, a multidisciplinary approach for streamlining the hazard assessment of emerging 2D materials is outlined, thereby providing a pathway for accelerating their safe use in a range of technologically relevant contexts.

Contribution of engineered nanomaterials physicochemical properties to mast cell degranulation

The rapid development of engineered nanomaterials (ENMs) has grown dramatically in the last decade, with increased use in consumer products, industrial materials, and nanomedicines. However, due to increased manufacturing, there is concern that human and environmental exposures may lead to adverse immune outcomes. Mast cells, central to the innate immune response, are one of the earliest sensors of environmental insult and have been shown to play a role in ENM-mediated immune responses. Our laboratory previously determined that mast cells are activated via a non-FcεRI mediated response following silver nanoparticle (Ag NP) exposure, which was dependent upon key physicochemical properties. Using bone marrow-derived mast cells (BMMCs), we tested the hypothesis that ENM physicochemical properties influence mast cell degranulation. Exposure to 13 physicochemically distinct ENMs caused a range of mast degranulation responses, with smaller sized Ag NPs (5 nm and 20 nm) causing the most dramatic response. Mast cell responses were dependent on ENMs physicochemical properties such as size, apparent surface area, and zeta potential. Surprisingly, minimal ENM cellular association by mast cells was not correlated with mast cell degranulation. This study suggests that a subset of ENMs may elicit an allergic response and contribute to the exacerbation of allergic diseases.

Amino Acid Analogue-Conjugated BN Nanomaterials in a Solvated Phase: First Principles Study of Topology-Dependent Interactions with a Monolayer and a (5,0) Nanotube

Using density functional theory and an implicit solvation model, the relationship between the topology of boron nitride (BN) nanomaterials and the protonated/deprotonated states of amino acid analogues is investigated. In the solvated phase, the calculated results show distinct "physisorbed versus chemisorbed" conditions for the analogues of arginine (Arg)- and aspartic acid (Asp)-conjugated BN nanomaterials, including a monolayer (ML) and a small-diameter zigzag nanotube (NT). Such a distinction does not depend on the functional groups of amino acids but rather depends on the curvature-induced interactions associated with the tubular configuration. Arg and Asp interact with the BNML to form physisorbed complexes irrespective of the state of the amino acids in the solvated phase. For the NT, Arg and Asp form chemisorbed complexes, and the distinct nature of bonds between the donor electron moieties of N_(Arg) and O_(Asp) and the boron of the tubular surface is revealed by the natural bond orbital analysis; stronger s-type bonds for the deprotonated conjugated complexes and slightly weaker p-type dominated bonds for the protonated conjugated complexes. The interaction of neutral Trp with BN nanomaterials results in physisorbed configurations through π-stacking interactions with the indole ring of the Trp and BN nanomaterials. The calculated results form the basis for a theoretical study of more complex protein macromolecules interacting with nanomaterials under physiological conditions.