Interactions between proteins and carbon-based nanoparticles: exploring the origin of nanotoxicity at the molecular level

Molecular Insights into the Binding and Conformational Changes of Hepcidin25 Blood Peptide with 4-Aminoantipyrine and Their Sorption Mechanism by Carboxylic-Functionalized Multiwalled Carbon Nanotubes: A Comprehensive Spectral Analysis and Molecular Dynamics Simulation Study

In this work, the main purpose is to analyze and understand the mechanism and thermodynamic interactions of carboxylic acid-functionalized multiwalled carbon nanotubes (cf-MWCNTs) and 4-aminoantipyrine (AAP) with human hepcidine25 (Hep25) using multispectroscopic and molecular docking modeling methods, binding free energy calculations, and molecular dynamics (MD) simulations under physiological conditions. AAP belongs to a class of persistent environmental contaminants, and its residue is a potential hazard to human health, exhibiting a high binding affinity with blood peptides. Hepcidin is a 25-residue peptide hormone with four disulfide bonds that regulates the iron balance in vertebrates and contributes to host immunity as a cysteine-rich antimicrobial peptide. Due to their diverse properties and pollutant absorption capabilities, CNTs demonstrate important biological effects in biological applications, particularly in the noncovalent interactions with blood peptides. A comprehensive molecular dynamics simulation integrated with molecular docking methodologies was employed to explore the binding free energy between AAP and Hep25, identify binding sites, elucidate thermodynamic characteristics, and evaluate the binding forces governing their interaction. The investigation delved into elucidating the precise binding site of AAP within the Hep25 protein and thoroughly analyzed the impact of AAP on the microenvironment and conformational dynamics of Hep25. The circular dichroism (CD) experimental results highlight a reduction in β-sheet composition following the introduction of AAP and cf-MWCNT. In addition, outcomes from fluorescence spectroscopy demonstrate that both cf-MWCNT and AAP significantly attenuated Hep-25 fluorescence via a static quenching mechanism. According to the MD simulations, the presence of AAP induces changes in the secondary structure of Hep25 and enhances its hydrophobicity. Additionally, our findings demonstrated that alongside the alteration in protein structure and functionality induced by contaminants, cf-MWCNTs possess the capability to mitigate the contaminant-induced effects on Hep25 activity while preserving the overarching structural integrity of Hep25. Based on the distance and RDF data, we found that during the simulation the presence of the cf-MWCNT causes the AAP to move away from the Hep25, and as a result fewer and weaker interactions of the AAP with the Hep25 will be observed. Likewise, free energy calculations indicate that the binding of Hep25 to AAP and cf-MWCNT involves electrostatic, π-cationic, and π-π stacking interactions. The research findings offer invaluable insights into the intricate influence of pollutants and carbon nanotubes on protein functionality within the circulatory system and their toxicity in vivo for prospective investigations.

Different functional groups of carbon dots influence the formation of protein crowns and pepsin characteristic in vitro digestion

Application of nanomaterials (NMs) in agriculture poses an ingestion risk to humans and may affect the digestive process. Different fates of NMs with differential charges in the gastrointestinal tract should be considered. In this study, the interaction between three carbon dots (CDs) carried with different functional groups (-NH2, -OH, and -COOH) and pepsin was analyzed through an in vitro digestion model. The results showed that CDs significantly reduced pepsin activity. Among them, CDs-NH2 had the greatest effect, following by CDs-OH, and CDs-COOH. Besides, molecular docking demonstrated the specific binding site of CDs to pepsin, while the most stable binding energy (-8.10 kcal/mol) was formed between CDs-NH2 and pepsin. Further, CDs formed a nanomaterial-protein crown structure with pepsin. The present study enriches the functional group properties of CDs in the digestion and provides new ideas for the potential human health of NMs.

Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.

Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure

Fluorinated graphene, a two-dimensional nanomaterial composed of three atomic layers, a central carbon layer sandwiched between two layers of fluorine atoms, has attracted considerable attention across various fields, particularly for its potential use in biomedical applications. Nonetheless, scant effort has been devoted to assessing the potential toxicological implications of this nanomaterial. In this study, we scrutinize the potential impact of fluorinated graphene on a protein model, HP35 by utilizing extensive molecular dynamics (MD) simulation methods. Our MD results elucidate that upon adsorption to the nanomaterial, HP35 undergoes a denaturation process initiated by the unraveling of the second helix of the protein and the loss of the proteins hydrophobic core. In detail, substantial alterations in various structural features of HP35 ensue, including alterations in hydrogen bonding, Q value, and RMSD. Subsequent analyses underscore that hydrophobic and van der Waals interactions (predominant), alongside electrostatic energy (subordinate), exert influence over the adsorption of HP35 on the fluorinated graphene surface. Mechanistic scrutiny attests that the unrestrained lateral mobility of HP35 on the fluorinated graphene nanomaterial primarily causes the exposure of HP35's hydrophobic core, resulting in the eventual structural denaturation of HP35. A trend in the features of 2D nanostructures is proposed that may facilitate the denaturation process. Our findings not only substantiate the potential toxicity of fluorinated graphene but also unveil the underlying molecular mechanism, which thereby holds significance for the prospective utilization of such nanomaterials in the field of biomedicine.

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.

Novel theranostic approaches to neovascularized atherosclerotic plaques

As the global burden of atherosclerotic cardiovascular disease continues to rise, there is an increased demand for improved imaging techniques for earlier detection of atherosclerotic plaques and new therapeutic targets. Plaque lesions, vulnerable to rupture and thrombosis, are thought to be responsible for the majority of cardiovascular events, and are characterized by a large lipid core, a thin fibrous cap, and neovascularization. In addition to supplying the plaque core with increased inflammatory factors, these pathological neovessels are tortuous and leaky, further increasing the risk of intraplaque hemorrhage. Clinically, plaque neovascularization has been shown to be a significant and independent predictor of adverse cardiovascular outcomes. Microvessels can be detected through contrast-enhanced ultrasound (CEUS) imaging, however, clinical assessment in vivo is generally limited to qualitative measures of plaque neovascularization. There is no validated standard for quantitative assessment of the microvessel networks found in plaques. Advances in our understanding of the pathological mechanisms underlying plaque neovascularization and its significant role in the morbidity and mortality associated with atherosclerosis have made it an attractive area of research in translational medicine. Current areas of research include the development of novel therapeutic and diagnostic agents to target plaque neovascularization stabilization. With recent progress in nanotechnology, nanoparticles have been investigated for their ability to specifically target neovascularization. Contrast microbubbles have been similarly engineered to carry loads of therapeutic agents and can be visualized using CEUS. This review summarizes the pathogenesis, diagnosis, clinical significance of neovascularization, and importantly the emerging areas of theranostic tool development.

Computational Biomaterials: Computational Simulations for Biomedicine

With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.

Computational Investigation of Chirality-Based Separation of Carbon Nanotubes Using Tripeptide Library

Carbon nanotubes (CNT) have fascinating applications in flexible electronics, biosensors, and energy storage devices, and are classified as metallic or semiconducting based on their chirality. Semiconducting CNTs have been teased as a new material for building blocks in electronic devices, owing to their band gap resembling silicon. However, CNTs must be sorted into metallic and semiconducting for such applications. Formerly, gel chromatography, ultracentrifugation, size exclusion chromatography, and phage display libraries were utilized for sorting CNTs. Nevertheless, these techniques are either expensive or have poor efficiency. In this study, we utilize a novel technique of using a library of nine tripeptides with glycine as a central residue to study the effect of flanking residues for large-scale separation of CNTs. Through molecular dynamics, we found that the tripeptide combinations with threonine as one of the flanking residues have a high affinity for metallic CNTs, whereas those with flanking residues having uncharged and negatively charged polar groups show selectivity towards semiconducting CNTs. Furthermore, the role of interfacial water molecules and the ability of the tripeptides to form hydrogen bonds play a crucial role in sorting the CNTs. It is envisaged that CNTs can be sorted based on their chirality-selective interaction affinity to tripeptides.

Molecular Dynamics Study of the Curvature-Driven Interactions between Carbon-Based Nanoparticles and Amino Acids

We researched the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional graphene (graphene33). Their curvatures decrease sequentially, and all of the CNTs are single-walled carbon nanotubes. We observed that as the curvature of CBNs decreases, the adsorption effect of the 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and "Benzene-like" Pro also have a strong adsorption effect on carbon-based nanoparticles.

Molecular and Macromolecular Interactions of Carbon-Based Nanostructures

The interactions of molecules and macromolecules with carbon nanostructures such as carbon dots, carbon nanotubes, graphene, graphene oxide, and fullerenes, have been stimulating the interest of the researchers working on the preparation, functionalization, properties and applications of carbon-based nanomaterials [...].

Interaction of Atomically Precise Thiolated Copper Nanoclusters with Proteins: A Comparative Study

A facile synthesis of glutathione-stabilized copper nanoclusters (CuNCs) is carried out in H2O/ tetrahydrofuran medium. The photophysical and morphological studies performed with as-synthesized CuNCs revealed the formation of green-emissive, stable, and smaller nanoclusters. The precise composition of these as-synthesized CuNCs was predicted with the aid of electrospray ionization mass spectrometry analysis as Cu12(SG)9. Furthermore, the systematic studies of the interaction of synthesized CuNCs with three plasmatic proteins, namely, bovine serum albumin (BSA), lysozyme (Lys), and hemoglobin (Hb) have been performed by using a series of spectroscopic studies. The conformational changes in these proteins upon interacting with CuNCs and their binding stoichiometries have been investigated from the combination of UV-visible and steady-state fluorescence measurements. The changes in the microenvironment of proteins caused by CuNCs were investigated by circular dichroism spectroscopy. Among these three proteins, BSA and Lys had a minor effect on the luminescence of CuNCs, which makes them suitable candidates for biological applications. There are no drastic changes in the microenvironment of NCs as well as proteins because of the possibilities of weak electrostatic and H-bonding interactions of CuNCs with BSA and Lys. The feasibility of strong metallophic interaction between the Fe2+ present in the heme group of Hb and Cu(I) or -S atoms present in the CuNCs brings considerable changes in the photophysical activity of CuNCs and their interactions with Hb. The functional groups on NCs as well as active amino acid residues present in proteins play a crucial role in determining their interactions. This work shed a piece of knowledge on designing NCs for specific biological applications.

Effects of multi-walled carbon nanotubes in soil on earthworm growth and reproduction, enzymatic activities, and metabolomics

Increased production and environmental release of multi-walled carbon nanotubes (MWCNTs) increase soil exposure and potential risk to earthworms. However, MWCNT toxicity to earthworms remains unclear, with some studies identifying negative effects and others negligible effects. In this study, to determine whether exposure to MWCNTs negatively affects earthworms and to elucidate possible mechanisms of toxicity, earthworms were exposed to sublethal soil concentrations of MWCNTs (10, 50, and 100 mg/kg) for 28 days. Earthworm growth and reproduction, activities of cytochrome P450 (CYP) isoforms (1A2, 2C9, and 3A4) and antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and glutathione-s-transferase (GST)), and metabolomics were determined. Effects of MWCNTs on earthworms depended on exposure concentration. Exposure to MWCNTs did not significantly affect growth and reproduction of individual earthworms. Exposure to 50 mg/kg MWCNTs significantly increased activities of CYP2C9, CYP3A4, SOD, CAT, and GST but clearly reduced levels of L-aspartate, L-asparagine, and glutamine. With exposure to 100 mg/kg MWCNTs, toxic effects on earthworms were observed, with significant inhibition in activities of CYP isoenzymes and SOD, significant reductions in L-aspartate, L-asparagine, glutamine, and tryptophan, and simultaneous accumulations of citrate, isocitrate, fumarate, 2-oxoglutarate, pyruvate, D-galactose, carbamoyl phosphate, formyl anthranilate, hypoxanthine, and xanthine. Results suggest that toxicity of MWCNTs to earthworms is associated with reduced detoxification capacity, excessive oxidative stress, and disturbance of multiple metabolic pathways, including amino acids metabolism, the tricarboxylic acid cycle, pyruvate metabolism, D-galactose metabolism, and purine metabolism. The study provides new insights to better understand and predict the toxicity of MWCNTs in soil.

Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation; that is, the target distribution function and the PMF potential energy are extracted, and then, the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have been through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.

Effect of dopamine-functionalization, charge and pH on protein corona formation around TiO2 nanoparticles

Inorganic nanoparticles (NPs) are gaining increasing attention in nanomedicine because of their stimuli responsiveness, which allows combining therapy with diagnosis. However, little information is known about their interaction with intracellular or plasma proteins when they are introduced in a biological environment. Here we present atomistic molecular dynamics (MD) simulations investigating the case study of dopamine-functionalized TiO2 nanoparticles and two proteins that are overexpressed in cancer cells, i.e. PARP1 and HSP90, since experiments proved them to be the main components of the corona in cell cultures. The mechanism and the nature of the interaction (electrostatic, van der Waals, H-bonds, etc.) is unravelled by defining the protein residues that are more frequently in contact with the NPs, the extent of contact surface area and the variations in the protein secondary structures, at different pH and ionic strength conditions of the solution where they are immersed to simulate a realistic biological environment. The effects of the NP surface functionalization and charge are also considered. Our MD results suggest that less acidic intracellular pH conditions in the presence of cytosolic ionic strength enhance PARP1 interaction with the nanoparticle, whereas the HSP90 contribution is partly weakened, providing a rational explanation to existing experimental observations.

Recent Progress of Novel Nanotechnology Challenging the Multidrug Resistance of Cancer

Multidrug resistance (MDR) of tumors is one of the clinical direct reasons for chemotherapy failure. MDR directly leads to tumor recurrence and metastasis, with extremely grievous mortality. Engineering a novel nano-delivery system for the treatment of MDR tumors has become an important part of nanotechnology. Herein, this review will take those different mechanisms of MDR as the classification standards and systematically summarize the advances in nanotechnology targeting different mechanisms of MDR in recent years. However, it still needs to be seriously considered that there are still some thorny problems in the application of the nano-delivery system against MDR tumors, including the excessive utilization of carrier materials, low drug-loading capacity, relatively narrow targeting mechanism, and so on. It is hoped that through the continuous development of nanotechnology, nano-delivery systems with more universal uses and a simpler preparation process can be obtained, for achieving the goal of defeating cancer MDR and accelerating clinical transformation.

Characterization of the selective binding of modified chitosan nanoparticles to Gram-negative bacteria strains

Chitosan is a nature-sourced polysaccharide widely used in numerous applications. The antibacterial potential of chitosan has attracted researchers to further develop and utilize this polymer for the formation of biocompatible antibacterial agents for both the food and healthcare industries. The tested hypothesis in this study is that modified N-alkylaminated chitosan nanoparticles (CNPs) have selective binding properties to Gram-negative bacteria strains that result in bacterial aggregation. Various bacterial strains were tested of five Gram-negative bacteria including Erwinia carotovora, Escherichia coli, Pseudomonas aeruginosa, Salmonella, and Serratia marcescens, as well as three Gram-positive bacteria strains including Bacillus licheniformis, Bacillus megaterium, and Bacillus subtilis. The fluorescence microscopy characterization showed that the presence of CNPs caused the aggregation of Escherichia coli bacteria cells, where modified CNPs with a shorter chain length of the substituent caused a higher aggregation effect. Moreover, it was found that the CNPs exhibited a selective binding behavior to Gram-negative as compared to Gram-positive bacteria strains, mainly to Escherichia coli and Salmonella. Also, the scanning electron microscopy characterization showed that CNPs exhibited selective binding to Gram-negative bacteria, which was especially understood when both Gram-negative and Gram-positive bacteria strains were within the same sample. In addition, the bacterial viability assay suggests that CNPs with a lower degree of substitution have a higher inhibitory effect on bacterial growth. CNPs with longer side chains had a less inhibitory effect on the bacterial growth of Gram-negative strains, where a concentration-dependent response pattern was only seen for the cases of Gram-negative strains, and not for the case of Gram-positive strain. To conclude, the further understanding of the selective binding of CNPs to Gram-negative bacteria strains may produce new opportunities for the discovery and characterization of effective antibacterial agents.

Self-assembly of ultra-small-sized carbon nanoparticles in lipid membrane disrupts its integrity

Although nanomaterials are widely studied in biomedical applications, the major concern of nanotoxicity still exists. Therefore, numerous studies have been conducted on the interactions of various biomolecules with various types of nanomaterials, including carbon nanotubes, graphene, fullerene etc. However, the size effect of nanomaterials is poorly documented, especially ultra-small particles. Here, the interactions of the smallest carbon nanoparticle (NP), C₂₈, with the cell membrane were studied using molecular dynamics (MD) simulations. The results show that similar to fullerene C₆₀, the C₂₈ NPs can self-assemble into stable clusters in water. Inside the membrane, the C₂₈ NPs are more prone to aggregate to form clusters than C₆₀ NPs. The reason for C₂₈ aggregation is characterized by the potential of mean force (PMF) and can be explained by the polarized nature of C₂₈ NPs while the acyl chains of lipids are nonpolar. At the C₂₈ cluster regions, the thickness of the membrane is significantly reduced by the C₂₈ aggregation. Accordingly, the membrane loses its structural integrity, and translocation of water molecules through it was observed. Thus, these results predict a stronger cytotoxicity to cells than C₆₀ NPs. The present findings might shed light on the understanding of the cytotoxicity of NPs with different sizes and would be helpful for the potential biomedical applications of carbon NPs, especially as antibacterial agents.

Carbon Nanotubes Promote the Development of Intestinal Organoids through Regulating Extracellular Matrix Viscoelasticity and Intracellular Energy Metabolism

The biological effect of engineered carbon nanotubes (CNTs) as beneficial biomaterials on the intestine, especially on its development, remains unclear. Here, we investigated the profitable effect of CNTs with a different graphene layer and surface modification on the 3D model of intestinal organoids and demonstrated that CNTs (50 μg/mL) promoted the development of intestinal organoids over time (0-5 days). The mechanisms involve the modulation of extracellular matrix (ECM) viscoelasticity and intracellular energy metabolism. In particular, CNTs reduced the hardness of the extracellular matrix through decreasing the elasticity and increasing the viscosity as a result of elevated metalloproteinase and binding to a protein scaffold, which activated the mechanical membrane sensors of cells, Piezo, and downstream P-p38-yes-associated protein (YAP) pathway. Moreover, CNTs altered the metabolic profile of intestinal organoids and induced increased mitochondria activity, respiration, and nutrient absorption. These mechanisms cooperated with each other to promote the proliferation and differentiation of intestinal organoids. In addition, the promoted effect of CNTs is highly dependent on the number of graphene layers, manifested as multiwalled CNTs > single-walled CNTs. Our findings highlight the CNT-intestine interaction and imply the potential of CNTs as biomaterials for intestine-associated tissue engineering.

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C₆₀. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol⁻¹, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol⁻¹ for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C₆₀ was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C₆₀ binding.

The interaction of folate-modified Bletilla striata polysaccharide-based micelle with bovine serum albumin

We fabricated an amphiphilic folate-modified Bletilla striata polysaccharide (FA-BSP-SA) copolymer that exhibited good biocompatibility and superior antitumor effects. This study investigated the affinity between FA-BSP-SA and bovine serum albumin (BSA) via multispetroscopic approaches. Changes in the morphology and particle size showed that FA-BSP-SA formed a blurry "protein corona". Stern-Volmer equation demonstrated that FA-BSP-SA micelles decreased the fluorescence of BSA via static quenching. The measurement results of thermodynamic parameters (entropy change, enthalpy change, and Gibbs free energy) suggested that the binding between FA-BSP-SA and BSA was spontaneous in which Van der Waals forces and hydrogen bonding played major roles. The results from synchronous fluorescence, circular dichroism, and UV spectra also revealed that BSA conformation was slightly altered by decreasing α-helical contents. In addition, the antitumor effects in vitro of Dox@FA-BSP-SA micelles and the cellular uptake behavior of micelles in 4T1 cells were decreased after incubating with BSA.

The Role of Exosomes and Their Cargos in the Mechanism, Diagnosis, and Treatment of Atrial Fibrillation

Atrial fibrillation (AF) is the most common persistent arrhythmia, but the mechanism of AF has not been fully elucidated, and existing approaches to diagnosis and treatment face limitations. Recently, exosomes have attracted considerable interest in AF research due to their high stability, specificity and cell-targeting ability. The aim of this review is to summarize recent literature, analyze the advantages and limitations of exosomes, and to provide new ideas for their use in understanding the mechanism and improving the diagnosis and treatment of AF.

Organoids: A new approach in toxicity testing of nanotherapeutics

Nanotechnology has revolutionized diverse fields, which include agriculture, the consumer market, medicine, and other fields. Widespread use of nanotechnology-based products has led to increased prevalence of these novel formulations in the environment, which has raised concerns regarding their deleterious effects. The application of nanotechnology-based formulations into clinical use is hampered by the lack of the availability of effective in vitro systems, which could accurately assess their in vivo toxic effects. A plethora of studies has shown the hazardous effects of nanoparticle-based formulations in two-dimensional in vitro cell cultures and animal models. These have some associated disadvantages when used for the evaluation of nano-toxicity. Organoid technology fills the space between existing two-dimensional cell line culture and in vivo models. The uniqueness of organoids over other systems for evaluating toxicity caused by nano-drug formulation includes them being a co-culture of diverse cell types, dynamic flow within them that simulates the actual flow of nanoparticles within biological systems, extensive cell-cell, cell-matrix interactions, and a tissue-like morphology. Thus, it mimics the actual tissue microenvironment and, subsequently, provides an opportunity to study drug metabolism and toxico-dynamics of nanotechnology-based novel formulations. The use of organoids in the evaluation of nano-drug toxicity is in its infancy. A limited number of studies conducted so far have shown good predictive value and efficiently significant data correlation with the clinical trials. In this review, we attempt to introduce organoids of the liver, lungs, brain, kidney intestine, and potential applications to evaluate toxicity caused by nanoparticles.

Probing the Interaction of Bovine Serum Albumin with Copper Nanoclusters: Realization of Binding Pathway Different from Protein Corona

With an aim to understand the interaction mechanism of bovine serum albumin (BSA) with copper nanoclusters (CuNCs), three different types CuNCs having chemically different surface ligands, namely, tannic acid (TA), chitosan, and cysteine (Cys), have been fabricated, and investigations are carried out in the absence and presence of protein (BSA) at ensemble-averaged and single-molecule levels. The CuNCs, capped with different surface ligands, are consciously chosen so that the role of surface ligands in the overall protein-NCs interactions is clearly understood, but, more importantly, to find whether these CuNCs can interact with protein in a new pathway without forming the "protein corona", which otherwise has been observed in relatively larger nanoparticles when they are exposed to biological fluids. Analysis of the data obtained from fluorescence, ζ-potential, and ITC measurements has clearly indicated that the BSA protein in the presence of CuNCs does not attain the binding stoichiometry (BSA/CuNCs > 1) that is required for the formation of "protein corona". This conclusion is further substantiated by the outcome of the fluorescence correlation spectroscopy (FCS) study. Further analysis of data and thermodynamic calculations have revealed that the surface ligands of the CuNCs play an important role in the protein-NCs binding events, and they can alter the mode and thermodynamics of the process. Specifically, the data have demonstrated that the binding of BSA with TA-CuNCs and Chitosan-CuNCs follows two types of binding modes; however, the same with Cys-CuNCs goes through only one type of binding mode. Circular dichroism (CD) measurements have indicated that the basic structure of BSA remains almost unaltered in the presence of CuNCs. The outcome of the present study is expected to encourage and enable better application of NCs in biological applications.

A Full Set of In Vitro Assays in Chitosan/Tween 80 Microspheres Loaded with Magnetite Nanoparticles

Microspheres have been proposed for different medical applications, such as the delivery of therapeutic proteins. The first step, before evaluating the functionality of a protein delivery system, is to evaluate their biological safety. In this work, we developed chitosan/Tween 80 microspheres loaded with magnetite nanoparticles and evaluated cell damage. The formation and physical-chemical properties of the microspheres were determined by FT-IR, Raman, thermogravimetric analysis (TGA), energy-dispersive X-ray spectroscopy (EDS), dynamic light scattering (DLS), and SEM. Cell damage was evaluated by a full set of in vitro assays using a non-cancerous cell line, human erythrocytes, and human lymphocytes. At the same time, to know if these microspheres can load proteins over their surface, bovine serum albumin (BSA) immobilization was measured. Results showed 7 nm magnetite nanoparticles loaded into chitosan/Tween 80 microspheres with average sizes of 1.431 µm. At concentrations from 1 to 100 µg/mL, there was no evidence of changes in mitochondrial metabolism, cell morphology, membrane rupture, cell cycle, nor sister chromatid exchange formation. For each microgram of microspheres 1.8 µg of BSA was immobilized. The result provides the fundamental understanding of the in vitro biological behavior, and safety, of developed microspheres. Additionally, this set of assays can be helpful for researchers to evaluate different nano and microparticles.

EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space

The transition network provides a key to reveal the thermodynamic and kinetic properties of biomolecular systems. In this paper, we introduce a new method, named effective energy rescaling space trajectory mapping (EspcTM), to detect metastable states and construct transition networks based on the simulation trajectories of the complex biomolecular system. It mapped simulation trajectories into an orthogonal function space, whose bases were rescaled by effective energy, and clustered the interrelation between these trajectories to locate metastable states. By using the EspcTM method, we identified the metastable states and elucidated interstate transition kinetics of a Brownian particle and a dodecapeptide. It was found that the scaling parameters of effective energy also provided a clue to the dominating factors in dynamics. We believe that the EspcTM method is a useful tool for the studies of dynamics of the complex system and may provide new insight into the understanding of thermodynamics and kinetics of biomolecular systems.

Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping

In recent years, nanomaterials have attracted considerable research attention for biological and medical related applications due to their well-recognized physical and chemical properties. However, the deep understanding of the binding process at the protein-nanomaterial interface is essential to solve the concern of nano-toxicity. Here, we study the interactions between the recently reported graphenic nano-sheets, BC3 and C3N, and a prototypical protein (YAP65WW domain) via atomistic molecular dynamics simulations. Our simulations reveal that elemental doping is an effective way to tune the binding characteristics of YAP65WW with two nanomaterials. While YAP65WW can be attracted by two nanomaterials, the BC3 sheet is less able to disrupt the protein structure than C3N. From the energy point of view, this is because protein residues demonstrate a binding preference with the trend from electron rich nitrogen to electron deficient boron. Structural analyses of the bio-nano interface revealed the formation of an ordered water shell on the BC3 surface, which was compatible to the crystal pattern of BC3. When a protein binds with BC3, these interfacial water molecules protect the protein from being disrupted. We suggest that elemental doping is efficient to produce fruitful biological-effects of graphenic nanomaterials, which make it a prospective solution for the future design and fabrication of advanced nanomaterials with desired function.

15 Years of Small: Research Trends in Nanosafety

In the field of nano- and microscale science and technology, Small has become one of the worldwide leading journals since its initiation 15 years ago. Among all the topics covered in Small, "nanosafety" has received growing interest over the years, which accounts for a large proportion of the total publications of Small. Herein, inspired by its coming Special Issue "Rethinking Nanosafety," a general bibliometric overview of the nanosafety studies that have been published in Small is presented. Using the data derived from the Web of Science Core Collection, the annual publication growth, most influential countries/institutions as well as the visualized collaborations between different countries and institutions based on CiteSpace software are presented. A special emphasis on the impact of the previous Special Issue from Small that is related to nanosafety research is given and the research trend from the most highly cited papers during last 15 years is analyzed. Lastly, future research directions are also proposed.

Theoretical modeling of interactions at the bio-nano interface

Ruhong Zhou, Thomas Weikl and Yu-qiang Ma introduce the Nanoscale themed issue on Theoretical Modelling at Biointerfaces.

A Robust Bioderived Wavelength-Specific Photosensor Based on BLUF Proteins

Photosensitive proteins are naturally evolved photosensors that often respond to light signals of specific wavelengths. However, their poor stability under ambient conditions hinders their applications in non-biological settings. In this proof-of-principle study, we grafted the blue light using flavin (BLUF) protein reconstructed with flavin adenine dinucleotide (FAD) or roseoflavin (RoF) onto pristine graphene, and achieved selective sensitivity at 450 nm or 500 nm, respectively. We improved the thermal and operational stability substantially via structure-guided cross-linking, achieving 6-month stability under ambient condition and normal operation at temperatures up to 200 °C. Furthermore, the device exhibited rare negative photoconductivity behavior. The origins of this negative photoconductivity behavior were elucidated via a combination of experimental and theoretical analysis. In the photoelectric conversion studies, holes from photoexcited flavin migrated to graphene and recombined with electrons. The device allows facile modulation and detection of charge transfer, and provides a versatile platform for future studies of photoinduced charge transfer in biosensors as well as the development of stable wavelength-selective biophotosensors.

Deposition of protein-coated multi-walled carbon nanotubes on oxide surfaces and the retention in a silicon micromodel

The aggregation, deposition and porous retention of bovine serum albumin treated multi-walled carbon nanotubes (BSA-MWCNTs) are investigated using dynamic light scattering (DLS), quartz crystal microbalance with dissipation (QCM-D) and 2-dimensional silicon micromodel, respectively. The aggregation of BSA-MWCNTs is consistent with Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The critical coagulation concentration (CCC) is 175 mM NaCl and 2.7 mM CaCl₂, suggesting that Ca²⁺ causes stronger aggregation. The BSA-MWCNT deposition on SiO₂ surface is unfavorable with critical deposition concentration (CDC) of 100 mM in NaCl and 0.9 mM in CaCl₂. The deposition on the Al₂O₃ surface is favorable. Deposition rate is dominated by electrostatic forces at low ionic strength (IS), but electrostatic interaction is eliminated when IS is above CDC. Therefore the deposition rate on SiO₂ or Al₂O₃ surface starts decreasing at the CDC point due to the reduced particle diffusion. In micromodel, the amount and position of attached BSA-MWCNTs in pore space can be observed by a microscope. The retention attachment efficiency increases at higher IS. The suspended BSA-MWCNTs approach to the collector through either diffusion or interception. The attached BSA-MWCNTs narrow the pore space and then clog the pore throats. The straining process happens on the clogged pore throats.

Nano-bio interactions: a neutrophil-centric view

Neutrophils are key components of the innate arm of the immune system and represent the frontline of host defense against intruding pathogens. However, neutrophils can also cause damage to the host. Nanomaterials are being developed for a multitude of different purposes and these minute materials may find their way into the body through deliberate or inadvertent exposure; understanding nanomaterial interactions with the immune system is therefore of critical importance. However, whereas numerous studies have focused on macrophages, less attention is devoted to nanomaterial interactions with neutrophils, the most abundant leukocytes in the blood. We discuss the impact of engineered nanomaterials on neutrophils and how neutrophils, in turn, may digest certain carbon-based materials such as carbon nanotubes and graphene oxide. We also discuss the role of the corona of proteins adsorbed onto the surface of nanomaterials and whether nanomaterials are sensed as pathogens by cells of the immune system.

Design of Small Nanoparticles Decorated with Amphiphilic Ligands: Self-Preservation Effect and Translocation into a Plasma Membrane

Design of nanoparticles (NPs) for biomedical applications requires a thorough understanding of cascades of nano-bio interactions at different interfaces. Here, we take into account the cascading effect of NP functionalization on interactions with target cell membranes by determining coatings of biomolecules in biological media. Cell culture experiments show that NPs with more hydrophobic surfaces are heavily ingested by cells in both the A549 and HEK293 cell lines. However, before reaching the target cell, both the identity and amount of recruited biomolecules can be influenced by the pristine NPs' hydrophobicity. Dissipative particle dynamics (DPD) simulations show that hydrophobic NPs acquire coatings of more biomolecules, which may conceal the properties of the as-engineered NPs and impact the targeting specificity. Based on these results, we propose an amphiphilic ligand coating on NPs. DPD simulations reveal the design principle, following which the amphiphilic ligands first curl in solvent to reduce the surface hydrophobicity, thus suppressing the assemblage of biomolecules. Upon attaching to the membrane, the curled ligands extend and rearrange to gain contacts with lipid tails, thus dragging NPs into the membrane for translocation. Three NP-membrane interaction states are identified that are found to depend on the NP size and membrane surface tension. These results can provide useful guidelines to fabricate ligand-coated NPs for practical use in targeted drug delivery, and motivate further studies of nano-bio-interactions with more consideration of cascading effects.

Consequences of Hydrophobic Nanotube Binding on the Functional Dynamics of Signaling Protein Calmodulin

The wide applications of nanomaterials in industry and our daily life have raised growing concerns on their toxicity to human body. Increasing evidence links the cytotoxicity of nanoparticles to the disruption of cellular signaling pathways. Here, we report a computational study on the mechanisms of the cytotoxicity of carbon nanotubes (CNTs) by investigating the direct impacts of CNTs on the functional motions of calmodulin (CaM), which is one of the most important signaling proteins in a cell, and its signaling function relies on the Ca2+ binding-coupled conformational switching. Computational simulations with a coarse-grained model showed that binding of CNTs modifies the conformational equilibrium of CaM and induces the closed-to-open conformational transition, leading to the loss of its Ca2+-sensing ability. In addition, the binding of CNTs drastically increases the calcium affinity of CaM, which may disrupt the Ca2+ homeostasis in a cell. These results suggest that the binding of hydrophobic nanotubes not only inhibits the signaling function of CaM as a calcium sensor but also renders CaM to toxic species through sequestering Ca2+ from other competing calcium-binding proteins, suggesting a new physical mechanism of the cytotoxicity of nanoparticles.

Oxidative Stress of Carbon Nanotubes on Proteins Is Mediated by Metals Originating from the Catalyst Remains

Nanomaterials introduced into biological systems are immediately coated by proteins in vivo. They induce oxidative stress on adsorbed proteins and hence alter the protein structures, which determines the fate pathways and biological impacts of nanomaterials. Carbon nanotubes (CNTs) have been suggested to cause protein oxidation. In this work, we discovered that CNTs induce oxidative stress on proteins in cooperation with coexisting metals originating from catalyst remains. Protein sulfhydryl groups were readily oxidized by the coexistence of CNTs and metals. Numerical simulations of the reaction demonstrated that the metals effectively mediate electron transfer between the CNTs and protein sulfhydryl groups. Thus, the coexistence of CNTs and metals, even in low concentrations, generates oxidative stress on proteins with high reaction rates. Metal catalysts used for CNT growth, in turn, catalyze the oxidation reaction of proteins. The proposed protein oxidation mechanism will advance the fundamental understanding of the biological safety and toxicity of nanomaterials synthesized using metal catalysts.

Biomimetic Carbon Fiber Systems Engineering: A Modular Design Strategy To Generate Biofunctional Composites from Graphene and Carbon Nanofibers

Carbon-based fibrous scaffolds are highly attractive for all biomaterial applications that require electrical conductivity. It is additionally advantageous if such materials resembled the structural and biochemical features of the natural extracellular environment. Here, we show a novel modular design strategy to engineer biomimetic carbon fiber-based scaffolds. Highly porous ceramic zinc oxide (ZnO) microstructures serve as three-dimensional (3D) sacrificial templates and are infiltrated with carbon nanotubes (CNTs) or graphene dispersions. Once the CNTs and graphene coat the ZnO template, the ZnO is either removed by hydrolysis or converted into carbon by chemical vapor deposition. The resulting 3D carbon scaffolds are both hierarchically ordered and free-standing. The properties of the microfibrous scaffolds were tailored with a high porosity (up to 93%), a high Young's modulus (ca. 0.027-22 MPa), and an electrical conductivity of ca. 0.1-330 S/m, as well as different surface compositions. Cell viability, fibroblast proliferation rate and protein adsorption rate assays have shown that the generated scaffolds are biocompatible and have a high protein adsorption capacity (up to 77.32 ± 6.95 mg/cm3) so that they are able to resemble the extracellular matrix not only structurally but also biochemically. The scaffolds also allow for the successful growth and adhesion of fibroblast cells, showing that we provide a novel, highly scalable modular design strategy to generate biocompatible carbon fiber systems that mimic the extracellular matrix with the additional feature of conductivity.

The impact of self-replicating proteins on inflammation, autoimmunity and neurodegeneration-An untraveled path

The central nervous system (CNS) in neurodegenerative diseases is a battlefield in which microglia fight a highly atypical battle. During the inflammatory process microglia themselves become dysfunctional and even with all the available immune arsenal including cytokine or/and antibody production, the battle is eventually lost. A closer look into the picture will reveal the fact that this is mainly due to the atypical characteristics of the infectious agent. The supramolecular assemblies of misfolded proteins carry unique features not encountered in any of the common pathogens. Through misfolding, proteins undergo conformational changes which make them become immunogenic, neurotoxic and highly infective. The immunogenicity appears to be triggered by the exposure of previously hidden hydrophobic portions in proteins which act as damage-associated molecular patters (DAMPs) for the immune system. The neurotoxicity and infectivity are promoted by the small oligomeric forms of misfolded proteins/peptides. Oligomers adopt conformations such as tubular-like, beta-barrel-like, etc., that penetrate cell membranes through their hydrophobic surfaces, thus destabilizing ionic homeostasis. At the same time, oligomers act as a seed for protein misfolding through a prion/prion-like mechanism. Here, we propose the hypothesis that oligomers have catalytic surfaces and exercise their capacity to infect native proteins through specific characteristics such as hydrophobic, electrostatic and π-π stacking interactions as well as the specific surface area (SSA), surface curvature and surface chemistry of their nanoscale supramolecular assemblies. All these are the key elements for prion/prion-like mechanism of self-replication and disease spreading within the CNS. Thus, understanding the mechanism of prion's templating activity may help us in the prevention and development of novel therapeutic strategies for neurodegenerative diseases.

Nanostructures of diamond, graphene oxide and graphite inhibit CYP1A2, CYP2D6 and CYP3A4 enzymes and downregulate their genes in liver cells

INTRODUCTION AND OBJECTIVE

Currently, carbon nanostructures are vastly explored materials with potential for future employment in biomedicine. The possibility of employment of diamond nanoparticles (DN), graphene oxide (GO) or graphite nanoparticles (GN) for in vivo applications raises a question of their safety. Even though they do not induce a direct toxic effect, due to their unique properties, they can still interact with molecular pathways. The objective of this study was to assess if DN, GO and GN affect three isoforms of cytochrome P450 (CYP) enzymes, namely, CYP1A2, CYP2D6 and CYP3A4, expressed in the liver.

METHODS

Dose-dependent effect of the DN, GO and GN nanostructures on the catalytic activity of CYPs was examined using microsome-based model. Cytotoxicity of DN, GO and GN, as well as the influence of the nanostructures on mRNA expression of CYP genes and CYP-associated receptor genes were studied in vitro using HepG2 and HepaRG cell lines.

RESULTS

All three nanostructures interacted with the CYP enzymes and inhibited their catalytic activity in microsomal-based models. CYP gene expression at the mRNA level was also downregulated in HepG2 and HepaRG cell lines. Among the three nanostructures, GO showed the most significant influence on the enzymes, while DN was the most inert.

CONCLUSION

Our findings revealed that DN, GO and GN might interfere with xenobiotic and drug metabolism in the liver by interactions with CYP isoenzymes responsible for the process. Such results should be considered if DN, GO and GN are used in medical applications.

Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

BACKGROUND

Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure.

METHODS

Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized.

RESULTS

Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch.

CONCLUSION

Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.

The Inhibitory Effect of Hydroxylated Carbon Nanotubes on the Aggregation of Human Islet Amyloid Polypeptide Revealed by a Combined Computational and Experimental Study

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.

Novel fluorescent antifolates that target folate receptors α and β: Molecular dynamics and density functional theory study

Nine novel fluorescent antifolates, 1-9, were designed and docked with FRα and FRβ. The binding energies of the bound complexes were determined by molecular docking and MM-PBSA studies. The structural properties of the complexes FR-FOL, FR-7, FR-8 and FR-9 were analyzed in detail via molecular docking and molecular dynamics studies. We further calculated the root mean square displacement and root mean square fluctuation of the bound complexes using molecular dynamics simulations. Since compounds 7, 8 and 9 are promising candidate in distinguishing FRα from FRβ, the hydrogen bond properties of complexes FRα-7, FRα-8 and FRα-9 were studied by a dispersion complemented density functional tight-binding method. The purpose of this study is to provide a rationale for the design of novel fluorescent antifolates targeted with FRα and FRβ.

The potential impact of carboxylic-functionalized multi-walled carbon nanotubes on trypsin: A Comprehensive spectroscopic and molecular dynamics simulation study

In this study, we report a detailed experimental, binding free energy calculation and molecular dynamics (MD) simulation investigation of the interactions of carboxylic-functionalized multi-walled carbon nanotubes (COOH-f-MWCNTs) with porcine trypsin (pTry). The enzyme exhibits decreased thermostability at 330K in the presence of COOH-f-MWCNTs. Furthermore, the activity of pTry also decreases in the presence of COOH-f-MWCNTs. The restricted diffusion of the substrate to the active site of the enzyme was observed in the experiment. The MD simulation analysis suggested that this could be because of the blocking of the S1 pocket of pTry, which plays a vital role in the substrate selectivity. The intrinsic fluorescence of pTry is quenched with increase in the COOH-f-MWCNTs concentration. Circular dichroism (CD) and UV–visible absorption spectroscopies indicate the ability of COOH-f-MWCNTs to experience conformational change in the native structure of the enzyme. The binding free energy calculations also show that electrostatics, π-cation, and π-π stacking interactions play important roles in the binding of the carboxylated CNTs with pTry. The MD simulation results demonstrated that the carboxylated CNTs adsorb to the enzyme stronger than the CNT without the–COOH groups. Our observations can provide an example of the nanoscale toxicity of COOH-f-MWCNTs for proteins, which is a critical issue for in vivo application of COOH-f-MWCNTs.

Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity

Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.

Probing nano-patterned peptide self-organisation at the aqueous graphene interface

The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.